Yes I think I see what you mean, this kind of thing can really get extremely complicated! :D
Where there is a need to combine different char based elements, ie. a 2x2 tile -set (and it's chars) and another simple charset, the best CharPad can currently offer is the option to manually copy/paste between projects.
ie. If project 'A' contains a tile-set (+chars) of your game's large letters and project 'B' contains your 1x1 alphanumerics (chars)...
..to combine them you could copy project B's chars, then load project A and paste the copied chars to the front of the charset.
The paste will push forward the existing chars (and automatically refactor the char references in the tiles) of project A.
This would give you a single charset that contains all of the images for your 1x1 and your 2x2 elements.
I'm sure you can appreciate just how complex this kind of thing can get!
At some point I may begin work on a separate tool that just deals with the problem of CharPad project combinations, although it would be better if such things could be done dynamically by the C64, then your game could shuffle things around as needed at run-time.
The thing you are asking for is kind of a Holy Grail!