As long as your tow vehicle can handle the added tongue weight (a pair of 6v deep cycle batteries can add up, depending on which battery you choose) and you consider their weight into the total weight load of the trailer (which also needs to include the weight of a full load of propane, and water if you take it with you) I don't see why you could not upgrade. You'll have to add a different battery box to hold them, but it should work. At the very least, I've seen others who have done this with a popup.
As far as battery choice, you'll hear a lot of different opinions on this (a pair of 6v v.s. a pair of 12v). One thing is certain though - a true deep cycle will be a better choice than a dual-purpose battery when you need a lot of amp hours.
1975 Westfalia (VW)
2014 Rockwood A122