Problems: 1. That's why in the SBS Essentials tutorial, I installed AC on a separate partition. Avoid installing programs on the main partition. As you mentioned it's only 60GB.
2. D is for documents and shares. Every users docs on the network are backed up daily to the server. C - Operating System (SBS 2011) D - Documents and Shares
My Preference: (Please watch the tutorial) C - OS D - Docs and Shares (Separate larger drive) E - Amazing Charts
3. SBS does hijack the drive. You can partition it after the fact though. I got about 200GB partition from a 2TB Backup Drive and 1TB on my SBS. I like to keep my backups on a separate power supply like those provided with external hard drives. You could get a 2TB External and leave the 1TB as internal storage. Or you can get an external enclosure for the 1TB drive.
4. If you can't run the wizard, then you can't set it up. It does not need to be activated to run the wizard. PM me and we'll go through the steps.
5. You just have to enter the license key and it'll be activated. No reinstall necessary.