making a flashable theme

I dont mean to look for the easy way out but ive searched and cannot find exactly what i am looking for. I want to turn my AOKP theme into a flashable zip and im not sure where to start.

Ive already edited the pngs, .9 pngs, and xmls i want and turned out a pretty nice red theme with full colored icons. I used the common apks; contacts, phone, systemui, settings, and framework-res. Where do i go from here?

I have found some threads saying you use the entire apk and just copy it into another theme, but im looking to do it from scratch. Also, that doesnt seem right to copy the entire apk over because that would overwrite any changes made in the nightlies. Wouldnt you just take only the drawables, values, etc out and make that the theme?

thanks for any help.