There are no "horror stories" about dual booting Windows Vista with Ubuntu. They both dual boot perfectly well. The only catch is that Windows Vista must be ideally installed on the FIRST PARTITION of your First HDD. WUBI is for people from Windows trying to figure "what is Ubuntu?". It in not a recommended way to install Ubuntu.
Originally Posted by noobman29
You say you have two Hard Drives (HDD), right?
Then I suggest that you install Ubuntu on the HDD where Vista is not installed. After successfully installing ubuntu you edit your BIOS settings to boot HDD on which ubuntu is installed to boot first. This way you can not only boot both Ubuntu and Windows, you retain your Windows MBR, Boot-loader intact.
If you have any more doubts then shoot...
"Evolution is Nature's way of issuing upgrades."