You should start your engine with the smaller (probably a group 24 battery) and then switch to "all". This allows a both batteries to be charged as your outboard is running and charing. After you stop, and are going to be at anchor, drifting etc, you should shift to the House battery. In your case the larger of the two.
There is a better way, that most of us use: That is to use an automatic combiner, called a voltage sensitive relay or automatic charging relay. This allows the engine to start on the proper battery, then as that batter begins to charge automatically switches to charge both batteries. They will be combined until the charging stops, and then will again isolate the starting battery,
You should have one one or two wires attached to the house battery. If there are multiple wires, you need to be using a positive and negative bus bar. All of the circuits should have a fuse within 7" of the battery. To start with, be sure that all terminals are bright and clear, including the negatives. Retighten the connections and then coat with a protective grease. (I use a product called corrosion block.)
Enjoy the "new" boat! Post some photos.