Hello,
Ok, firstly.. the sprites in those cells do not need to be empty/blank, instead they need to contain (references to) sprite image *zero*, ie. the very first sprite in the set (it is a good idea to keep it blank).
You can use the Sprite Brush tool to paint sprite images into the cells of a tile.
You may also find it helpful to use the compressor to make sure only one blank is present (in the sprite-set) and used in the tiles...
ie. If you are pixelling tiles by hand then decompression is enforced/necessary before you can do this which will make every sprite-cell (in the tile) refer to a different sprite image, so try compressing when you have finished pixelling (to make all the "blanks" use sprite zero and that will let you see the expansions).
I hope that helps!