Two banks of two batteries - different size - no-no?

If you plan to charge them off the same charger or to use them together at the same time, they also will need to connect to the charger/house system with the same length/same size cable. If the cable to the new batteries is a different length, the batteries on the longer cable will never charge fully, and will discharge to a different depth than the originals, which will cause problems down the road. From the sounds of it, you will have to do the switchover thing.