Hi, thanks for your suggestion,
Something like this (a sprite layer) has been on the todo/maybe list for quite a while, the idea has just taken a back seat to the more char-related features (of which there is, and has been, an enormous amount to do).
I'm sure at some point there will be a merging between SpritePad and CharPad to turn the tool into more of a programmer's "level editor" than the tile-map editor that it currently is.
The idea is on the list!