umm I see what you mean BMR. I do have a perfect solution when it comes to your second point. Wonder if you've visited vbulletin.org, but it is possible to list Mysidia and MA as separate categories but on the same forum. Some big boards of multiple functionalities do this, this is somewhat of a preview but slightly different:
http://www.vbulletin.org/forum/showthread.php?t=175687
This way it will make things quite clear which is the section MA-related questions are supposed to be asked and answered. Also if I havent explain this before, all MA's current staff will remain and I will not be involved in the forum general management since I believe they have enough experience to handle forum issues and constructions. But of course, I will do the basic house-keeping stuff like you always did, such as adding/removing subforums, promoting/demoting staff, getting rid of spambots/trolls and anything the MA staff cannot do. Lemme know if you have any more questions or concerns, I can see how you are trying to make it comfortable for MA staff and members, which is definitely no problem.
If the back-end admin functionality is so tightly integrated with MyBB, is MA forum like forever stuck with MyBB forum too? It may be a real problem though, for any potential MA buyers I mean, since most would prefer either vbulletin or IPB.