I was wondering if someone could point me in the direction of which program is the best for creating themes.
to create a theme, you must change the .png files within the hdpi folders in framework-res.apk. i know of 2 ways to do that. the first would be with ninjamorph. that allows you to replace files one by one, which could be quite time consuming. aside from that, you could use a program called apk manager and pull the apk to your computer, extract the files, replace them with files of your choosing with either photoshop or something similar (gimp is popular), rezipping, and pushing back to your phone.
all theming i have done has been with apk manager. please be sure to make a backup before starting as messing with framework-res can screw up your phone.