The VSR in the end parallels the batteries making it one big battery.
You must also have a selectable battery switch and keep it on Batt 1 ( start batt) not on 1+2 which is a mistake many people make.
Stick with the manufacturers supplied battery chemistry. Different chemistry requires different charge requirements to get the best out of them. Many outboards now offer a dual battery circuit direct from the alternator so might be worth checking if your ski has that option as it means both batteries would be charged independently direct by the the alternator makng the vsr pointless.
The question to ask the ski manufacturer is what is the amount of free amps avaliable from the alternator and it's duty cycle. As a general rule 5-10 times the free amp output was what I was always told was reasonable battery size to have and have charged in a reasonable time. . So 10 amps free , 50% cycle is 5 amps and 5 to 10 times is 25-50 amp hour battery it should support.