It is fascinating to me that there are so many different ideas about how to set up what should be fairly straightforward.
Two things have emerged here that I had no idea about going into the project:
1. There is no way to keep AC from making automatic backups in its own folder, and no AC native routine for clearing out the old backups. This seems like an oversight, because I have more than once gotten error messages that backup "failed" -- and it turns out that the partition the AC program on was full. This will inevitably happen, even if the thing is running on a monster drive, because it takes about 3G or more for every backup. I figured this out myself -- but I can imagine it would be frustrating to an AC user who didn't care much about computers, and just wanted to get his/her charts done. I will look into the auto-remove ideas that both of you have mentioned.
2. SBS Essentials arbitrarily partitions the main drive (and doesn't invite changing partition sizes, though perhaps it could be forced.) The C partition is relatively small, and obviously is meant to be mainly for the operating system itself. D drive has folders for the clients, so it is obviously some sort of working space for the SBS system. The "folders" presumably are meant to contain "data", like documents generated by the clients -- most SBS users are likely to be non-medical offices who generate reports and the like that are different for all users, but stored on the server D drive (and maybe also locally? -- that part doesn't matter to me, we aren't going to use it that way). AC is different-- all users share a common database, which is forced onto the C drive so far as I can tell, and might not put anything at all into the SBS "folders" on the D drive, so it is probably bigger than it needs to be, at least for our implementation.
Also, the automatic backup of SBS (which in their default setup occurs at least twice per day) a separate hard drive is required, which simply "disappears", presumably visible only to the SBS system itself, avoiding screwups by people putting things on the backup drive. It looks like AC .enc files could be added to "automatic backup" by SBS itself, but I haven't got that far. If so, then yet another drive for internal backup would be unnecessary, and the AC backup program could be used only for external backup.