They are supposed to be over the seat mounted, and wire tied to the brackets. This makes the pillion seat unusable (too hard)
What I did was take off the seat, cut out a square on one side of the over the seat strap to avoid the regulator, and tighten up the strap they supply.
At first I tried velcro to attach the bags to the brackets, because the loops on the bags were now too low to make sense as an attachment point. That didn't hold well, so I drilled holes in the bags and bolted them to the brackets using wing nuts. That worked a charm.

As already stated, they are over the seat, just put them on the rear seat. I have the stock bags and since I ride solo its no big deal. I use nylon stringing to attach to the brackets. They hold well but also release the knots relatively easy for cleaning and such.  

I have a set of the OEM bags and I mount them under the seat. Just make a snall notch out for the rectifier so it doesnt cover it up. I'm going to be getting a different set soon tho, I got the OEM's with the bike when I bought it and I really dont care for them to much. They are very narrow around 3.5" if I remember right and they dont hold much. From looking around most seem to run around 6" wide like the ones on my girlfriends bike, hold much more and are easier to get stuff in and out. Just an FYI...

Darren