If I tie the positive side of my starting battery into the positve side of my trolling battery, will the rectifier be able to charge both batteries? I know that the rectifier doesnt put out a high amp charge, but would it be enough to keep my trolling battery from going down? I hardly evey use my trolling motor and im not asking if it will charge the trolling battey completely up if it is dead, but rather keep it charged so it is ready when i do want to use it. The motor the rectifier is on is a 40hp

What make amd model? I know my 50 wont do it. Its only a 6 amp stator.

2000 year model johnson 40hp

First off, both terminals need to be connected. Hook up the batteries as you normally would....but add a jumper between the + of each battery as well as the (-) of each one. Use LARGE wire, #6 or better. I dont know the output of that alternator, but if it's like 6 amps or so...it will probably be ok.
I did it on a 1972 Johnson 50 HP years ago and had no trouble.
***Just make certain that they are identical batteries for best results.***

But I would NOT do it with a deep cycle and a starting battery, for instance.

One of the pro techs on here will know more.