NexusTarget :
Xubuntu Is on the D: and Windows 7 Is on The C: and i intend to encrypt Both Drives Via Xubuntu
You have to encrypt windows in windows otherwise you'd be unable to open anything while working in windows. It would also block Xubuntu from opening them.
Is your goal to be the only one that can view the Windows drive when
running Linux?
Or do you want files that only you can access whether in Xubuntu or Windows? If that is the case, I've not done this but it should work, make a compressed/password protected folder in windows and put your files in it. They'll be password protected at both ends. It's not encryption but at least more secure.