I find leaving a small gap (less than 1/16") between the rails gives you some play for alignment. I use a 6' level or you can use the factory edge of your sheet goods. It's tempting to really tighten the set screws down, don't, you will dimple the rail. Besides they don't need to be more than snug, just check the alignment once in a while during the project, readjest when needed. David is right, if you find good pairings, mark them. Good luck.