The stock baffles supplied by V&H were the "cheese grater" variety--they're not going to do much about sound, and IMO not much either way about power, either.
Each muffler body should have two holes toward the end. One is for the baffle (innermost) and the outer one is for the optional billet "hot tips" available from V&H in several designs.
If I were you, I'd not bother with the stock baffles.
I've run three baffles in mine over time. The stock ones from V&H, Khrome Werks HP-Plus drag pipe baffles (2 1/4"), and now V&H "quiet" baffles. The Khrome werks baffles worked well, didn't seem to negatively affect power at all but did give a boost in mid-range RPM's. They also provided a pleasing cat's purr inhale rumble between gears. They have an interesting design of a sleeve with a welded-in core of linked spheres made of steel mesh. I could hear the difference in less and different noise and feel an increase in mid-range throttle response.
The V&H quiet baffles are quieter and provided a definite boost in low end torque over the KW. Not the same mid range and the sound is a bit different. The cat's purr is gone between gears, but I like the low end torque. I can't tell that I've lost much if anything elsewhere in the RPM range but I don't dyno these things so who knows? Seat of the pants is what I'm talking about. I have the V&H baffles in now, but Ikept the Krome Werks'.
V&H told me via e-mail that their quiet baffles (V21869) would not fit original StraightShots exhaust but I did some detective measuring and they fit just fine. Just a hair loose, if anything, but if that bothers you then have a muffler shop expand the rear opening a bit with their spreader. Me, I just bolted them in. I would recommend wrapping the fiberglass packing with wire before installation to keep the packing from blowing out so soon.
Understand, when I talk about quieter, I'm not talking about huge differences. The stock V&H cheese graters were loudest, a slight reduction came with the KW, and another slight reduction came with the V&H Quiet Baffle. It still sounds like a Harley.