Specific Dual Boot Question

I have searched the boards and have not found a clear answer to this question (want to make sure I don't lose all my stuff). Here goes...
I built my computer in January and I purchased/installed OEM XP Pro. I received a free Vista Business upgrade but have never used it. I decided to install it as a dual-boot set-up using 2 seperate hard drives, but the 'clean install' method does not work properly with the upgrade version of Vista. You can only install and demo it for 30 days as a clean install, but it won't let you activate it as a clean install (you must install it as an upgrade in order to activate it, or so said the message that popped up on my screen when I tried). It dual-booted fine, but Vista would have been inactive after 30 days.

So then, I removed Vista from Drive2, formatted it and install XP on Drive2 (XP now on Drive1 and Drive2; dual boot screen working fine; did not plan to activate on Drive2 before upgrade [do I need to?]). I want to upgrade to Vista strictly on Drive2, but I'm worried. It told me that I have to run the upgrade through XP, not by booting into the DVD, which I understand. However, if I boot to XP on Drive2 and install Vista as the upgrade, will it fool with XP on Drive1 at all? [BTW, I don't want to unhook the other drive during install, because that makes the dual boot thing screwy] I'm thinking it won't because I'm booted into Drive2, but I have never done this before. I need Drive1 to stay with XP Pro, and I don't want to lose any data (most is backed up, but still).
So, to sum up the question: does upgrading an install of XP to Vista on 1 drive of a dual-boot system fool with the XP on the other drive? Any help is GREATLY appreciated! Thank you!