It's been a little while since I've used it (so I don't remember ALL of the workings) but it requires a command prompt (time to remember all your DOS commands).
Once there, I believe that it tells you the parameters it requires when you type MLExtender or maybe MLExtender/?. It's a little tricky at first...I don't recall the help being very clear.
I always had it in its own folder and wrote a batch file to process whatever map I copied there.
My batch file had one line "mlextender d:\uo\uo" (I don't like excessive path typing).
I think it would create an output folder and put the converted map into it...but I don't remember clearly.
Edit:
Yeah, just tried it. When you write a small batch file for MLExtender, you don't need the command prompt. You just need to copy the map file to the folder, double click the batch file, and (provided the batch file is correct) it will convert the map file. It will NOT create an output folder. It overwrites the old map with the updated map. The path is the location of the map file. I just made it easier on myself by having MLExtender in the same folder.
Another Edit:
Word of caution though. This new region is made of some mysterious UO Ether. I recall having issues when I'd visit. Best if you have Centred and fill in all the space with black land tiles (or are they called void tiles?). Or I suppose Grass...for Green Acres. Then you can visit without issue.