http://bluesea.com/category/105/27/productline/119 is really what I was thinking you would use. Switches and fuses in one neat little package. This would allow you to install the proper size fuse for what ever the switch is attached to.
So a nice clean install would be a 8 gauge wires (since it is so short of a run 10 gauge should be plenty) from Bat + and - sides to their own covered bus bars (Never hook +and - to same bus bar). http://bluesea.com/products/2720. See last paragraph to use master battery switch.
All the - wires from any accessories (GPS,Bait pumps, nav lights) would be connected to the - side of bus bar.
All the positive wires from from any accessories (GPS,Bait pumps, nav lights) would be hooked to the switch panel. http://bluesea.com/category/105/27/productline/119
The switch panel is hooked to the + side of the bus bar at appropriate terminal. This is where any accessories (GPS,Bait pumps, nav lights) get + from. 10 gauge should be plenty for this short run.
If you want the switches to light up you need to also connect - to appropriate terminal on switch panel to - side of bus bar. http://www.go2marine.com/docs/mfr/bluesea/198878F.pdf
If you want to have a battery switch then connect TM, Jack plate, and + bus bar with to one side and + battery wire to other side. This should leave you with just 4 wires hooked to the battery. Tm, jackplate, and - bus wire on negative side. And one positive wire to battery switch, I'd make this 4-6 gauge.
You are right the fuse panel is used to decouple the fuses from their switches.