I've had Ubuntu 11.04 to 11.10 on my PC, and just upgraded to 12.04 LTS. I didn't realize that there was capabilities to install it along side with Windows. So now I'm downloading 12.04 with Windows Installer. Should I UNINSTALL the Ubuntu version that's currently partioned? (Windows installer = wubi)
no, it's easier to just install the new version on the same partition when you install. If you press advanced settings in partition you can change what part of the partition you want to use.
I suppose the "Windows Installer" you refer to is Wubi - if it's not I'm sorry.
As wubi is installed somewhat like a normal programme in Windows it should be save not to uninstall your previous Ubuntu versions.
However, since Wubi fiddles with the bootloader you might experience some issues you might not like. Unfortunately I don't know what your bootloader/grub etc. look like. But since you seem to have gotten along with Windows and Ubuntu side by side in a dual boot setup, you should be fine.
If you do not want your old install(s) of Ubuntu anymore, I suggest you get rid of them after you've made sure 12.04 LTS on Wubi is what you want. But be aware of your bootlader, do not mess it up.