On my cherokee I did not get real crazy about getting it perfect. My dad put the SYE kit on his and had to change the shims in the leafs a few times to get it right. He's pretty picky about any vibration though, I just wanted mine close enough that the u-joints did not go out all the time.
But to answer your question, I think most of the SYE manufacturers recomend that you rotate the pinion. Mine was already rotated up quite a bit due to really long shackles I had, and it just happened to be pretty close to where it needed to be.