BeastX & Atom 500 setup - newbie needs help

[CSwinton]

I just got the AR7200BX for my new Atom 500 and am having some difficulty understanding the best way to set everything up. Before installing the Receiver/BeastX unit, I had used the swash leveling tool that came with the kit to get as close as I could to 0 degrees on the blades (required very minor trim of one delrin rod). I then sized my links and installed them, adjusting the rod lengths to keep the cyclic servo arms horizontal (as much as possible). OK so far??

My confusion comes with how to best adjust the cyclic center when setting up the BeastX. Once I enter that setup, the servos all seem to recenter and are no longer in the positions they were when I used the swash leveling tool. Do I just try to readjust the servo arms via the BeastX cyclic trim setup to be as close to horizontal again? I understand the BeastX setup, I just can't seem to reestablish the same centering/default pitch that I had when doing the simple mechanical setup with the swash leveling tool.