Eric - yours is a very generic question so I'll offer a very generic answer. I'd look for a place with the following characteristics:
- Dry and out of the way
- Conveniently located for charging when the engine is running and use when powering the trolling motor
- Located where they improve the boats balance (e.g., toward the front and opposite where people and the fuel are)
It's not likely there is one spot that meets all of the above criteria, so you'll have to decide based on your particular boat configuration what takes precedence.