If I run wire for my depth finder power wire along side my trolling motor power wire will I get interference?  I will run them to seperate batteries.

I have my TM wires and depth finder wires cable tied together for about two feet at the battery box. They share a battery and I haven't had any issues. I am no electronic genius though and if you are running the wires for a longer distance you might run into some issues. You might want to check the mfg. website to see if they have installation requirements.

you would have to have much larger load and voltage to have to worry about interferance. The EMF on 12 volt DC is virtually non existant