Question about master & slave drives

Hey all, just a little background info here. Not sure if this is more appropriate in another part of the forums but it seems to fit the best here. A while ago I tried setting up a VPN connection (other thread about it here http://forums.majorgeeks.com/showthread.php?t=196182 if you care) and no matter what I tried I couldn't get it to work at all. So, I found another hard drive lying around and decided to see if it would work on that, and it did, so it seems pretty likely that something is up with Windows on the master drive or something, I obviously have no idea.

Anyways, the main question here is can I run a program completely from the slave drive (E while having booted up from the master drive (C? For example, I installed Windows and all the necessary stuff along with Hamachi on the E: drive earlier, and I tried booting up from the C: drive and running it from the E: drive. Wasn't expecting it to work that much, and it didn't (same error and everything), so is there any way I can make it work? I'm not really too hopeful about it either because even if there is a way it might just be more trouble than it's worth to set it up. I know I could just boot up the computer from the E: drive but I might as well just re-format the C: drive if that's the only way.

Thanks in advance for any possible help.