I find its much easier to work on your pc, do your thing inside the appropriate .apk res folder, reinsert into 7zip, update archive and then flash the update.zip. Of course I do a anadroid first.
I tell you Ardch has been a godsend from the beginning for helping me start my first theme. Thanks My Man!
I also have apk manager, but I havent got into it that much yet. I guess I need to start optimizing my .apk's.
Just as a side note, I'd add 7zip as a tool. I use it all the time, makes updating an archive a breeze.