Is there any way to send MMC commands with the A-Pro Editor? I use FL studio and I'm trying to link basic commands like pause, play, etc. I know the MMC numbers associated with these, like 6 for record and 1 for stop, would there be any messages I can send from my controller to mimic this?

Yes, just set them up as SysEx. See my other post on getting the A300 working with Reaper, I included some examples. Why Roland couldn't have added this capability to the software I have no idea, but it is, at most, a minor annoyance I guess.