People deal with this in different ways. It all depends how low you put the body on the frame, as well.
You can raise the bed 2" and lower the fenders on the bed, but this is not my favorite. It sounds like you have a 54-early 55 bed if yours has the contour on the bed side.
What we've always done with the S-10 swap (done about 5 now) is put the bed in the factory location and raise the bed floor. You only lose about 4" of bed floor in most cases, and it works out just fine.
I don't like the look of a raised bed, they don't look right in my opinion, and you can't do it without lowering the fenders on the bed sides.
