Most importantly, if you really have two different size batteries (a 200 amp and a 100 amp as bank1) connected in parallel, you have a problem even before considering the charge rate.
Change this first so you have equivalent batteries. Should be easy enough to just switch out the 100 amp o be used as a start battery and connect both 200's in parallel.
There is no problem having two different sized batteries in a single bank. They just need to be the same type - AGM, wet cell, or gel cell.