i use a rapid transit recon 19 tank bag its good for the small things ex: phone,GPS, smokes,extra visor,your favorite carry gun,map pocket and it has 3 external pockets and two internal pockets . I also use a Firstgear Silverstone tail bag its big enough to fit your helmet in. it has an expansion ziper, 3 outside pockets, and a velcro storage divider.

 

Since I brought it up figured I would try it. Couldn't get the seat to lock (tho its not going anywhere if your sitting on it ) with both straps under the seat.
However, I put one strap under the seat and the other behind the grab bar and it gave more room for passenger's legs and seat was able to lock. This could work. The issues you might have are... bags touching the pipe (I have a shorty no problems here, but looks like stock pipe might touch), and decreased brake and turn light visibility.
I bet you could find some saddle bags (smaller than mine) that would work well with the straps under the seat. I would use mine this way in a pinch (you know like a supermodel has to get a ride somewhere and I have the bags on )