It's just so you don't have to lug the whole sidecase/hardbag into the hotel room. You fill the soft bag, (don't overstuff it, the zippers tend to blow out), then it fits into the sidecase, (w/o room for anything else if it's full). It's kinda awkward to get inside the soft bag when it's in the hard bag w/o it falling out of the hard bag.
I use one on trips for my clothes and bathroom stuff. The other is loose with jacket liner, extra gloves, first aid kit, water, etc.
Note that there is a Left and a Right soft bag. The Yamaha logo faces out. They fit better if you use them that way. It is possible to pinch part of the soft bag in the hinge and the hard bag won't close correctly, so use care.
edit: They don't latch in, but there are straps that have a small q/r buckle that could be used to hold them in. I generally use the straps for the loose stuff and not for the soft bag. That's just me though.