My 2-bank BPS charger instuctions say that i should only charge 2 batteries together that are of the same type. I only want to charge my deep-cycle trolling motor baterries but one has a reserve of 225 min. and the other has a reserve of 115 min.Can i still charge these batteries together even if the brands and reserve times are different ?

Batteries of the same type mean both be flooded lead acid batteries like you have, or both be AGM, etc.   However, that much difference in size and it might cause the charger to have problems.  That charger is designed to transfer charge current to the weaker battery as one battery reaches full charge and it may try to bounce back and fourth with batteries that much difference.  You could call the tech support about that one.

Now, with that said, why are you running two different size batteries????  That's only damaging the batteries.  The smaller battery can not begin to maintain the charge level of the bigger battery so the bigger battery is doing all the work.   Two batteries connected together, series or parallel, should be identical in all aspects for best service, even the same age.   Anytime you replace TM batteries, replace the pair.