Lets see...
for the confusion over which pipe goes where: the smaller diameter pipe(the one on top in wyatt's picture) is the one that goes to the turbo, the larger diameter goes to the throttle body.

as to whether or not you have to cut the pipes: most people with newer kits shouldn't have to cut their pipes i have heard. I have like one of the first kits, so my pipes fit like ass. i cut both the pipes and got some silicone connectors and it fit a lot better.

as to losing that bead: if you gotta cut your pipe, just take a pair of plyers, bend the edges out on the edge of the pipe to make your own bead. It ain't quite as nice as a factory bead, but it works fine. I did that on mine as well as my buddies GST that i built all the intercooler pipes for his starion intercooler for. Just make sure you don't have really sharp edges or it will cut the silicone connectors.

hope this helped,
jason
95 GS turbo
Star Stage II
Unorthodox racing Stage 1+ clutch
Hoping to be first person with standalone ECU