The most important thing to do is to drop a marker(lock in place) at each side of the area you are working on. As you are discovering(the hard way), if you move any marker, everything past it is going to also move, so you need to place markers to prevent that(much the same way that when you Shift-click on a marker and move it, the markers on either side will lock in place, so ONLY the one you move, actually moves.
I use X-Form almost exclusively. If you have tried it, you probably hate the way it takes time to render, even if you simply click on a marker(without moving it). My solution is to choose just the area that needs work(and usually just what fits on my EDIT screen), separate that clip(region) and drop warp markers at each end(so the ends are locked in place). Then, I can move things around in this defined area, and because its only a few bars in length, it renders in a few seconds.
