K.i.s.s.
Personally, I would run the main and kicker motor on one battery, then isolate the other battery for the rest of the boat. Reasoning that you can simply attach both motors to one battery without any isolation and either would always charge that battery and then pass the rest of the amperage through the isolator to the other battery.
You might get electronic "noise" on the fish finder if you decide to run it with the trolling motor, depends on how good the finder is. They normally draw very little current, which in my case I run my finder and GPS through the main battery.
Regarding the battery, you should get as large as possible, dry (Optima type) deep cycle battery, the constant "cycling" or draining of a normal lead acid battery will kill that battery in fairly short order. I use two dry batteries from a forklift, they weigh close to 80lbs each for my trolling motor. Also make sure you put a charger on the second battery set-up every time you finish, because the main motor alternator will not likely fully charge it in the time back to the dock.
http://www.napaonline.com/Search/Detail.aspx?R=BK_7821769_0006398311
This has been used in motorhomes for years without fail. All you need in a simple battery isolator, the version I've attached from NAPA is rated up to 95 amps, which, unless you have a abnormally large alternator, would work fine.
Make sure you use at least 6 ga. cable, preferably 4 ga., do not skimp on the cable, otherwise you will increase resistance which can lead to heating the cable to the point of melting. If you're going to balance the boat and place the battery forward, make sure to grommet any holes, regardless if this is an aluminum or glass boat, the vibration will eventually wear through the cable sheathing. Get good COPPER eyes, that can be crimped AND soldered, after crimping the cable correctly, take a propane torch and heat the ring end to wick the solder all the way into the base, as opposed to heating the cable and opening of the ring that is visible. No special tools needed for crimping, just a good dull drift punch and a vise.