The optimum rig will see the trolling motor on a separate battery on it's own circuit.
For the house/starting power, your battery or batteries (two batteries are always better than one unless your boat is very small) should be connected positive to a battery switch, negative directly to the motor negative and on a separate 8/10ga wire to a negative buss bar. From the battery switch, connect the motor positive and on a separate 8/10 ga wire directly to a positive buss bar. From the positive buss bar, wire all accessories to a fuse or breaker, then to a switch (if required), then to the accessory. From the accessory, wire back to the negative buss bar. If you have a lot of accessories in the bow or stern you may want to install extra negative buss bars in those locations to avoid running lots of negative wire. Connect any aux negative buss bar directly to the main negative buss near the battery with 8 or 10 ga wire. If you run a jack plate or trim tabs don't scrimp on the wire to the buss bars. To keep things organized and maintainable, use the proper wire code colors for everything. You can find the code colors online. Good marine wire is tinned and 12 ga will work for most accessories.
For the trolling motor, I always use 6 ga, a 12 volt motor actually draws more current than a 24 or 36 volt, and bad wiring and connectors can easily cause a fire. From the trolling motor battery positive, wire in a 40 amp fuse or circuit breaker then positive to a heavy duty plug. Negative from the TM batterie(s) directly to the plug. USE A GOOD PLUG, cause that's where most fires start. Here's the plug I like: http://www.amazon.com/Battery-Tender-027-0004-BK-Trolling-Connector/dp/B002UCLJG0
Depending on your motor and gauges, most of the wiring will come thru one cable to a plug and then to a wiring harness for gauges, neutral switch, ignition switch, horn, etc. The only wiring that may be needed other than hooking up these various motor controls is instrument lights which should be wired just like any other accessory.
Good luck