You will inevitably hit lower with 3 under than split if you use the same anchor point, if you are shooting instinctively. For example, if you anchor with your middle finger in the corner of your mouth, the nock end of your arrow will be about 1" higher with 3 under, while the point end will be the same, so of course the arrow will shoot lower. Generally, if you are grouping well, it means you are shooting well, and you just have to bear with it for a while until your brain adjusts. The arrows will move up the target without you having to do anything specific about it. It helps to start close to the target where the difference isn't so great, and move back as your brain adjusts.
When you change your anchor, as most people do who try Rick's method, it doesn't seem to be as hard to adjust. In his school, the first arrow I ever shot using 3 under was also the first arrow I ever shot using his recommended anchor. Maybe the location of his recommended anchor counteracts to some degree the difference between 3 under and split.
Rick recommends adjusting the nock point, but there is very little adjustment you can do with the nock point without creating porpousing. That is more of a fine tuning technique after everything else is working right - maybe to get two bows to hit in the same place. He also recommends trying different shelf material. Leather, velcro, and fleece on the shelf all have an effect on where the arrow hits. But again, this is fine tuning - maybe moving the groups up or down an inch or so at 20 yards.