@zombeerose
I found using the create jsb pointed to a URL was the simplest.
I've had the sencha create jsb working with my stuff with beta 1 and 2 as well as 1.2.3 version of Sencha command sdk tools.
I'll find the post where I talk in more detail about it.

http://www.sencha.com/forum/showthre...l=1#post763129