So, you are doing it correct. You want them as parallel to the ball guides as possible. Ignore the holes. Once you think you have them aligned, push them both up and make sure they are even together. Then roll a ball down the guide a few times. Is it perfectly smooth? If so, you are done. If not, redo the alignment. The goal is perfect smoothness from ball guide to flipper, otherwise it's horrible to play. Also, make sure to gap them properly with gap tool