Depends on your machine. If it can manage the export and import of the full map, and it can work with a 3 layer PSD file of size 18944x7296 (you do the math), you'll be able to edit the map in a whole.
Otherwise, you'll have to do it part by part, depending on your machine limit (larger parts, more demands performancewise).
You made a good point however: I have no way to create an empty map ATM: I'll include a /create option in mextract to create an empty map instead of extracting the existing map.