Okay....So just so I am clear.
1. Marinco trolling motor plug that comes into my camper via the outlet in my bed via my engine battery.
A. Your isolator can be between the plug and your house battery or between the plug and your truck battery. Both will work. Fuse both ends.
2. Power and ground (with running lights) arrive to my fuse block in the camper that has running lights etc tied into it.
B. I have my running lights coming from the truck lighting and fused separately. How do you turn them off if powered off your fuse panel? Running lights require a separate wire from the truck lighting so they will go on and off with the truck lighting.
Here is where I get confused....
Would I simply:
1. install isolator in existing wiring under hood.
See A above
2. attach leads to house battery (12v) They are currently attached to the fuse panel.
House battery should power your camper fuse panel, one set of wires. IF you have a camper main power switch it should on on these wire going to the fuse panel. The wires from marinco plug should go to your battery can be through your isolator if you mount it in the camper. NOTE: if you have the truck wire going to your fuse panel it would change the camper battery, just not the right way to do it. Also your main disconnect switch would not function properly.
3. run new wire and attach leads to existing fuse panel so as to still have functionality to my running lights etc...
See B above.