So, since the tilemap requires more advanced editing of large numbers of sprites, the old method became rather impractical. I've been working on a revamped editor with a better interface to help with this - I'll have a beta ready today or tomorrow, but just in the interest of getting some feedback here are some screenshots:
The first screen is when editing an empty collection.
The second shows editing one sprite.
The third, a multi selection of sprites.
I'm not too happy about how the multiselection editing works right now, but its probably a necessary evil as the data isn't as clear cut - eg. I wan't to be able to draw a polygon collider and apply it to the rest of the selection too.
As usual, any feedback is appreciated.