Once the peep gets seated; if it still doen't line up, you can sometimes play with a little twisting of the bowstring to get it perfect. Also, if it still doesn't want to cooperate, you can just tie your string loop in (tight) to be rotated the same amount as the peep - so that, at full draw, they both wind up in the same plane.

For me, there is certain perfect spot for the peep relative to the nocking point. If I adjust it up or down, even 1/8", something just isn't right.