Well, do not be surprised. It is not enough info in your post.
What kind of motor ?, how many HP ?,
?, It is going to be on the low REV range ? right ?Now, You have two batteries, imagine that one is at 20% another at 80%., both require different current (amps) to be charged correctly, but your "kicker motor" can suply only one kind of current ( at trolling speed it will be pretty low)
Somebody has suggested that there is no problem charging batteries with his "Honda 90 hp for years". I do not question this at all, but do you have 90 hp kicker used for trolling on very low REV ?
Bottom line is that ( in my opinion ) main battery ( start ) should be charged from main motor ( not kicker ), other one should be charged from dedicated charger in your garage. And from time to time both should be toped - up from independent charger ( off water ).
If you insist of doing it the way you described it in your question, it will be rather expensive and very complicated