I can't say I know what works best in Biscayne. But going to the Keys, back when I was younger, sure you could throw out a handful of shrimp cut into 3 to 4 pieces and wait on them. Years later, with all the guides moving in and the fishing pressure getting more and more, things started to change. Sure you could call up some smaller bones and of course, all the pinfish and trash fish in the area, not to mention multiple small sharks, but the bigger more smarter bones will avoid you. Of course, you could chalk it up to the fact that there are not any decent bones in that area, but that is not always true.
Look, my goal here is to help you avoid the need for having to chum. But if you must, for the reasons you have or the ones I described below, then here is a stealthier approach than just chuckin bait out behind the boat.
Now mind you that with all the years of fly fishing I've done and many more than that spin fishing, if by myself, I just don't chum for anything. But sometimes If I have someone with me that is a novice fisherman, kid, family member, friend, etc and they want to target them... and with me, not being down there to the Keys for a while and not being on top of the fish movement for a while and want to see if any are around and not necessarily entice them by regular chumming, but want to do something more effective (for me anyway) I'll do the following;
The first thing I'll do when coming onto a spot that holds bones, is to start off trying not to chum in the 1st place, even tho I have those other anglers with me. Of course, approach the spot as dead stealthy as possible. That means cutting that motor way before you go onto the flat. Then if you have a TM, then TM to a point and then get on the pole and ease up to the area and the spot you want to target.
I'll set up, uptide of the area I know that they should be there. I basically sit and wait, scoping out the area for any signs. During this time, if you have any shrimp in the live well, cut it off. I'm saying "turn off your livewell!" As much pressure that they have these days, livewell pumps will turn them off and push them out and away from you, especially in shallow and skinny water. That can be different if you are spin fishing cause with 10lb braid, you can get many times the distance than with a fly line and with that, they are less prone to be turned off by a livewell pump at that distance. But nevertheless, I'll still turn any and all pumps off. ~laughs~ Imagine a fish of a lifetime bone or perm come within casting distance only only to have then automatic bilge pump switch kick on and blow your chances of that fish of a lifetime. Ask me how I know learned that fact!
So the key is to be stealthy and compare it to bow hunting vs rifle hunting. So the trick is to be as quite as possible so you drawl them in closer. So turn the pumps off and believe it or not, if you only have a couple dozen shrimp, they will last quite a while with the pump off, especially if the water temps are still cool and less than 80 degrees.
That being said, those larger Keys bones (and I'm sure very similar to Biscayne bones) are getting very educated these days. Stealth! No boat noise! Be set and ready. No fumbling around the boat getting ready. Probably the best way to get as close as possible to them to fly cast to them is to quietly wade out to that area if possible and then just wait for them. But if not, then set the boat up tide from where they will come onto a fly and in an area where it looks good or you think they will be. It really doesn't matter the tide, as long as there are moving water. If, in the beginning incoming tide, then be more to the edge so you can see them when they come on to the flat and then slide across the flat cross current. For me, that's the best time to get them to eat, especially early in the a.m. Later on during an outgoing, be closer in towards the back country side of the flat and catch them coming out from the interior holes of the flat and running towards the edges, again working their way across the current to catch any smells they may have missed.
So don't set up directly uptide from that spot you want to target them, but off to the side, so they are not directly feeling the movements of the boat and don't see you straight up ahead of them. Instead, you need to set up off to one side or the other from your targeted spot, depending on currents, where the sun is and where the winds are coming from. In other words, scope it out, use your head and pick the best spot to be the most stealthy and be able to make the best cast in.
IF YOU HAVE A POWER POLE..... resist using it! Why? Once down, yer wide ass end of the stern of the boat will be facing into the current and causing a ton of water to push around the boat, as well as water turbulence and water noise against the boat. All those things will turn those spooky bones off. Why? Cause they'll just feel it! Sure, you may fool the little guys, but not the bigger, more sharper fish. And if there is a perm around, then for get it! Also, forget about using a trolling motor of any kind, ESPECIALLY with a spot lock! That'll turn them off quicker than anything and they'll disappear before you see them. So instead, streamline the boat into the current and use a stick pin at the bow with a little release rope, or use a small backup anchor (even a small mushroom anchor) with a small diameter rope, just to hold the nose of the boat into the current (less water drag and noise). Or you can use someone on the PP sitting down on the PP and holding the boat in the current, holding it steady and still and just waiting on those fish.
If you still feel the need to call them up with chum, then you may be counter-productive throwing handfuls of chopped up shrimp at them cause the spookier ones will know something's up. And if you call them in that way, they will be jumpy/edgy and will blow up if they see something out of place. Also, by broadcasting handfuls of shrimp or shrimp pieces, you create a wide fan of scent that broatcast all over that flat, drawling in every pinfish on the flat and other trash fish, there in a big ball waiting for more handouts. So the scent will come and go in waves, as you throw it and every piece gets immediately eaten and then nothing until the next handful. You may actually miss bones swimming crosscurrent (as they do) in-between scent waves. If you happen to drawl in 1 or a few bones this way, they'll be going all over the place looking for it and you'll have a much harder time targeting them with a precise cast, jig or fly presentation.
Wait!!! Did someone in this thread just say he opened a can of tuna and then....

Lol
Instead, if you must chum (for those reason above), then yes, use fresh live shrimp only! (nothing dead or frozen). Cut them up into small 1/2" pieces (3-4 pieces per shrimp, depending on shrimp size), give each piece a light squeeze and throw it up tide towards the spot. So the idea is to throw it, one piece at a time, where the pieces will drift and land basically in the uptide side of the spot, sand spot or hole where you want them to come into. This is the point where you need to be patient but have your angler ready to cast when a fish comes into sight. So one piece at a time, you are flicking it out in the very exact same spot every time. Then each piece is drifting down into that very same location, every time. One at a time, long pauses between each piece you pinch/crush and throw into that exact same spot. Are you getting this?? The pauses can be anywhere from 30 seconds to 1 minute apart, to as much as 2 mins between pieces. This can depend on water depth and volume of current flow. What you basically want is between 30secs to 1 min of time (1 minute on avg) at the bottom of where you want the piece of bait to sit before the next bait is thrown. Even if something crushes and eats it, that scent will still be disperse in that same thin ribbon of scent. The main thing is, once you figure out your timing, stick to it, even if you think you see something coming, tell your caster to get ready and then when to cast, all the while you are not breaking your rhythm with the pieces of bait. Once you break that rhythm, you have to start it back up or wait a bit and move to another spot. So you are giving your spot a good 15-20 mins with about 4-6 shrimp total usage of fresh live bait at each location/spot. With about 2 dozen shrimp, that can give you about 4 to 6 solid areas to set up and chum, if need be. That, my friend, should be plenty.
So what does this do differently than throwing handfuls of chopped up bait? This exact rhythm method of a precisely placed piece of bait, one piece at a time in a very uniform manner will create a thread or thin ribbon of scent and will go along way across the flat, not all over the flat. You'll notice that baitfish trash generally hold in an area and broadcasting smell all over the flat will attract lots of them. But with a thin ribbon of scent, maybe only a few pins will come to investigate, that happens to be in that thread, but the rest will not. So you may see a few, but not many. Also you'll notice that bonefish will swim crosscurrent while coming onto or going off a flat. This allows them to catch any scent trails/scent ribbons and then follow it back to the source.
The end results will be fish that can be called further away from your targeted spot and you can look up ahead and see them coming. Then you can forecast where they will end up and pre-plan your cast and give the fly time to settle there when the fish arrives. Once there, you can start working it.
I hope my 2 cents of scents made sense to you!
Ted Haas