You could do what you are suggesting, but to what end? It seems to me you'd have a much greater chance for something to go wrong. Here are a few things to think about:
If you are running your trolling motor off of both, there is the distinct possibility you'll drain both batteries and then you'd be stranded. Keeping them independent will help ensure this won't happen. Your primary battery should be like what you'd find in a car, which provides a quick discharge with high amperage. The one you are using for your trolling motor should be a deep cycle battery, one which will discharge over a much longer period of time. While they could be tied together, you really don't want to do this.
Another thought is you probably should be running your aerator off of the trolling motor battery. For the same reason as stated above, you can drain your primary battery, again, leaving you stranded. Wouldn't be pretty either way.
You need to charge the one which does the trolling, which means disconnecting it on a regular basis to get it done. Keeping it separate will help in that endeavor, I'd think. The other one will probably be charged by the main boat motor, so you don't have to worry about it as much.