Flower Pot for Windows does not changes registry or anything like that. It just copies Flower Pot to your computer. You can simply move the installed FlowerPot folder to different location.
The path issue you described is probably caused by WinUAE itself. You might want to try the "Reset to defaults" or "Portable mode" button in WinUAE/Paths tab when running your original WinUAE installation. Or check its support forum here: http://eab.abime.net/forumdisplay.php?f=5
I am sorry for the inconvenience.