Is there some way to fill more than one "square" at once?

If not, i think this would be a great feature to add. Simply becouse, when im making a map for my players, i always try to make it as quick as possible. i think this would also be a great way to expand the way Shmeppy works.

tl;dr can you implement a way to colour more than one square?

Yes. Holding shift will let you fill/clear a rectangle all at once.

filling

Hovering over the fill tool with the toolbar expanded will show you all the different capabilities of the fill tool.