The EQ2MAP updater detects custom UIs using your EQ2.ini and installs only into your current UI (it'll only make and update the "EQ2MAP" folder in /UI if the updater is run when you're using the default UI). I just tested this myself.
It sounds like you may be confusing the "eq2map" and "eq2map2" folders inside your UI/CustomUIName folder with UI/EQ2MAP. To my knowledge, all UIs designed to work with EQ2MAP include eq2map and eq2map2 folders inside of them. It's how EQ2MAP is setup to work.
I'm not exactly sure what you're asking (it's tough to make out exactly what you mean in your post). But if your custom UI is installed and configured properly, all you have to do to update your POIs & maps is run the EQ2MAP updater. It will update the files inside your custom UI's folder (mainly in /images and /POI).
The way the game works, unless you set up some symbolic links (which allow one folder to exist at multiple paths) one UI cannot reference another custom UI, only the default UI when pieces do not exist in the custom UI. So your custom UIs (Profit, Drums, or any) cannot be drawing from UI/EQ2MAP. Instead the EQ2MAP updater updates the files within say UI/ProfitUI/. It will not update and will not even create a UI/EQ2MAP folder unless you run it when you have the default UI selected in your EQ2.ini (or just don't have an EQ2.ini).
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