Noise generated from the trolling motor is most likely coupling back into the fish finder by way of the tying of the powers together. This is a common thing. Proper filtering adds cost to a product so it is a corner typically cut on most consumer products.
The most immediate solution is to separate the batteries so that the fish finder is now isolated from the trolling motor. However I suspect that your buddy doesn't want the hassle of having to deal with moving the battery maintainer around. Another possibility is to put a selector switch in line with the maintainer which would then permit easy selection of the which battery is being maintained. Simply rotate the selector every couple of days.
Your buddy should be able to purchase a power line choke which should reduce the amount of noise the trolling motor throws out onto the power lines.
On another note, batteries in most situations are not meant to be ganged directly in parallel and you mentioned that is what your buddy has done. I would suggest another power topology. For example the simplest would be a single battery which is sized appropriately to handle all the power requirements. Power topology aside however the power choke still needs to be there to remove the noise when everything is all electrically interconnected together.