Removing multiple copies of SH3

[AngusJS]

I used multiSH3 to make two installations - one vanilla and one with GWX 1.4. I would like to get rid of the vanilla installation.

I have made it to early '44 playing more or less DiD, so I want to be sure that I won't affect my GWX copy before I proceed. Do I use Add/Remove programs? Do I uninstall using the splash screen menu? Or do I manually delete the folder from Program Files?

Thanks