I usually prefer to use Tile Molester and export the stuff I want to edit to a picture file, then use GIMP to do the actual drawing, then you can do whatever you want. A program like GIMP has way more features. Then you can import it back to TM when you're done.
TM also has a lot of flexibility with choosing how many bytes are in a row/column, as well as every format you can imagine. I confess I haven't used YY-CHR, because I've never needed to look beyond TM.