And if you want to avoid the minor issues westfw referred to, you can edit the preferences.txt - the one in the "lib" folder - for each IDE, and remove the comment mark before "settings.path=data". i.e.
# if you don't want settings to go into "application data" on windows
# and "library" on macosx, set this to the alternate location.
settings.path=data
This will put your user preferences.txt in the "data" folder in each IDE.
(You may have to make the "data" folder and copy a preferences.txt into it.)
Doing this allows for wildly different Arduino IDEs on the same machine. :.