Well, certain microphones from MF can't be used on the Avatar pieces that you add via x-drum because they don't exist for the avatar kit. I would stick to using the snare mics provided in MF if you want the kit to gel right. You should be able to use the condenser mics for the top and bottom snare, and it should show up in all of your individual drum mics, OHs and ambient mics. It won't show up in the mono mics or the chamber mic because those are specific to the MF kit. Once you set up your kit with all your bleeds and everything how you want it to sound, programmed all your notes/MIDI nodes, you should save your kit as a combined preset under the load/save tab. This will keep everything, including your microphone assignments, mixer, mapping, tool settings (everything) as a preset you can pull up.
There was a time I used the Avatar mics within the MF kit, but it just didn't sound right. I didn't care for it so now I try to use only mics within the kits I'm using.