So my 05 1800sr3 has one battery but looks like it can hold 2 or should have 2. Question I have is if I put a second battery in there how do I hook both of them together?
No they should be wired to a battery selector switch which has four positions, off, batt 1, batt 2, and both. The negative of both batteries will be tied together to the engine block.
You can start by looking at Blue Sea Systems battery switches. They have some videos and literature that explain what the switches do and how to hook them up.
Batteries
Linear Mode
