Haven't totally got my head around the entire thing but so far here are some thoughts on it.
1) If you don't have a run play in your formation, you won't have a "down" formation audible
2) If you don't have a play that the game considers a quick pass, you won't have a "up" formation audible (obviously same applies for PA & Deep Pass in general)
3) Strangely had a Strong I - Normal Corners Strike considered as a PA... had several plays I thought would be deep passes and none of them were picked up for the "right" formation audible.
4) The theory of removing all running plays except for the one you want as your "down" formation audible, saving your playbook, then reloading and adding run plays back will not work.
To test the theory, I removed all run plays from Strong I Normal except FB Dive. Saved, went to practice to test, FB Dive was "down" formation audible. Went back into playbook, added in HB Toss (so as not to confuse it with the default down audible, HB Dive). Saved it, went back to the practice field and HB Toss was now my new "down" formation audible.
Like I said... still trying to get my head wrapped completely around it but best I can tell you won't necessarily be able to "customize" your formation audibles like some had hoped. Obviously you'll still have formation audibles so long as you have a play that matches the criteria, just not any customization in my experience so far.