What exactly is it that you're asking?
You can only have 1 UI folder active in EQ2 at any one given time, and the EQ2MAP updater will automatically try to update the maps in your currently active UI. You don't need to separate it out or anything, if it's overwriting something you don't want it to just add that item to your eq2map_ignorelist.xml.
Are you using multiple different UIs at different times (i.e., swapping UIs when you swap characters)? If that's the case, you could always look into using symbolic links to tie the eq2map folders inside each UI together so that you'd only have one actual folder for it and the rest just symbolic links to it.