You're facing a problem that most of us have with a majority of the rests on the market. Hoyt and Bowtech in particular have the berger holes mounted rather low, with Bowtech being lower to the best of my knowledge. Most rests will not setup properly and have the arrow pass through the center of the hole. The best you can do is gain clearence on the shelf for the rest first, then see where the arrow falls in relation to the holes. I like mine to run through the center or even a below true center if I can. The Limb Driver will allow this and maybe a couple others.

Don't fret too much though. Spot Hogg once stated that it is not that important to pass perfectly through the center. A well tuned bow will shoot well regardless. They should know, they do their tests through a Hooter Shooter.