What motor do you have, and what else is drawing power? While underway, you shouldn’t drain and deplete a battery that badly. IF power assist is not being sufficiently powered, you should feel the power assist kicking out. If you are not feeling that, I wouldn’t think power assist is not behind your issue. There are others in here much more on top of these sorts of topics and hopefully they will chime in soon. Also, do a power assist and battery drain search in the upper right hand corner. There have been some topics on this, but they were focused not on batteries draining like this as much as power assist not getting enough juice to operate properly.
All of that said, something’s off here with battery #2 as this is not a normal issue.
FYI: if you look through the forum you’ll see very mixed and diverse views on if you should run only on 1 battery or the other or 1+2. Our dealer stresses running our tritoon, with all its electronics, on the 1+2 position for normal operation. I am unclear on if one or the other is better, or if it might depend on your boating habits (anchoring and play radio all day when not under way, or typically operating electronics when otherwise under power with the motor).
Again though, if you are running 1+2 typically, you should not have this issue with battery #2 going dead unless they don’t have it connected properly and its not getting the recharge from the motor/alternator (assuming you are not sitting with motor off playing radio or running electronics constantly off that battery only).