Yes I left them where they are because you get that little mounting tab to fasten them down to the frame. Generally speaking it is not a good idea to have your exhaust suspended solely from the flanges. Vibration stresses over time can cause the exhaust studs to become brittle, crack, and break off leading to severe exhaust leaks (like when you are riding on the interstate and your header pipe falls off and gets run over by a f*#%ing semi-truck) and/or leaving you with studs busted off flush with the head... where you'll need to drill/tap and ez-out (or not-so easy EZ-out) I dont have a decent camera or I'd take a pic right now, just have my stupid smart phone and haven't figured out how to add photo from it yet...
basically your stock pipes are a pipe inside a pipe. the inner one is smaller than you'd think. They come down to a tapered collar where the mufflers are attached. The header pipes go about 6 inches past the tapered collar inside the mufflers and then stop-- the body of the muffler serves as a sort of am expansion chamber and a resonator with a baffle at the outlet end. They are all mechanical, there is no packing. The skin of the mufflers is like .064" thick and if you cut with your die-grinder wheel about a half inch downstream of that tapered collar you can remove the entire muffler and leave just the head pipes... let me see if I can get a pic up...