Again, I don't use SBS 2011, but I think you have to get away from this folder thing. I suppose you could put things in there, but the data drive is for data. For instance, on ours, we have the databases for AC, the Medware folder, F.A.P faxes, subfolders inside a folder for transfers, etc. All-in-all, probably 20 things. A folder for a user, which I would use redirected, would take maybe 30 Mbs.
AC can easily be installed on the D: drive or even the 1 TB drive. There is a place in the install where it says where it will be put, and you either browse to a different drive or, more easily, just change the C to a D.
EVERYTHING that is important should be on the server. If you can put the Quickbooks databases on the server, then it should be on the server. If you biller's computer crashes, bye bye Quickbooks. This is what servers are for. A central computer for everything. Look at it this way. You want it so that if EVERY client crashed, you wouldn't blink an eye.
You can change the default backup to once a day. I do it at night. I don't see a need to do it twice a day. A bit of overkill, plus it has to slow down the server. Generally speaking, you have to choose volumes for SBS Backup. Just do your regular small backups for Medware and AC, and then let SBS back up everything. Once the hard drive is made, you can back up many, many whole servers. I have like 100 on mine. It is incremental, which can be changed.