Actually, you can overwrite all the tilesets if you prefer. For the tilesets, such as found in A tab.... Make sure that you are using the exact same dimensions as the different tilesets that make up the A tab. If you go to the Resource Manager and export TileA1 - TileA5, you can edit them as you see fit. When you are happy with what you do, import them to the same place and they will automatically overwrite the TileA1 - TileA5 that you import. If you like import only your custom designed TileA2 and want to use all the rest, import that one and you will see TileA2 in red and the others will remain in blue. It will automatically change on the A tab. Of course, if you open a new game it will be back to default once more. You can do the same thing for all of them. TileE (make sure to designate it as TileE) is much the same way, I don't know the exact limit pixelwise, but you can import and try it out.
Hope that helps!
KS
PS - Went back to test it out and it appears that the limit for TileE would be 512x512. That sort of sucks because if you need more you are screwed unless you do some heavy duty editing of other tilesets.