It all depends if your are 2 linkin it or 4 link. The parallel 4 link will require you to cut off the fron perches. The 2 link, you can use your stock or lowered ones I think. I actually cut the rivets out and moved the perches closer to the cab. This let me use a longer link bar giving me a better ride. Plus, the stock perches are lower than the frame, so if you don't move them up, you will be laying perches before frame.
So to answer your question, you should be fine with lowered or stock perches for a 2 link, as long as you relocate them.