Well, you could do separate maps like in Looney Tunes Collector: Alert!
After looking at the maps from Alert!, I was surprised to see that the overworlds are nearly identical. It makes Marvin Strikes Back! look like a lazy ROM hack. Furthermore, the Alert! overworld map probably has overlapping screens in the same places. And, since there's only one version of the Alert! overworld available on the site, those extra screens aren't represented.
If you were referring to the submaps (houses, caves, etc.), then yes, those could be in separate maps like you suggested.
My main concern is being able to represent the entire overworld, overlapping screens and all, without ruining the look of the map.
However, I might just be making a fuss over nothing. In my notes it's written that walking east from (8,3) on the overworld would bring you to an overlapping screen (an extra overworld screen shown before entering the house seen on (9,3)). However, I just went there in-game and can't reproduce it. I don't know if that's because I imagined the whole thing or if it's because I cheated to get to that area. It's been several months since I last looked at this game.
I might try to finish mapping this game on the grounds that I could have imagined the whole thing. It might be a while, though, since progress is slow on my current mapping project (a game that has a really weird map format).