Not having used FOG to deploy another OS apart from windows, I can at least confirm for you that if you choose multiple partition single disk, it will back up the MBR and restore it too. What I use is 1 Windows 7 64bit OS that joins our domain, and a second Windows 7 32bit that is standalone and I use the multi partition single disk option myself for this.
I also know that if you have just one copy of windows on a drive that the single partition option will do the same, even though windows 7 usually installs a 100meg partition at the start of the disk, this is included in that option.
As for the virus stuff, there is actually an option under task management to set a client pc scanning for viruses using clamAV. When you et it off to scan it reboots the pc, starts in clamav mode and goes looking on the internet for the latest signatures which it downloads and uses on the fly.
Hope this helps.