I go by formation and try to use the same formations in a variety of ways. For example you usually do a lot of passing from the shotgun, and I do. But I also run a lot of draws and play action from it too. As well as mixing run/pass plays from the I formations.
GT: TA JKGrizzle By day she drives the garbage truck. By night she becomes Papa Nebo, the hermaphroditic oracle of the dead.
Very simply, the best playcaller will force the defense to guess pass or run by mixing it up.
When they call a run defense and you pass, or they call a pass defense and you run, you'll have success. Plays that look like they could be either a pass or a run leave the defense guessing right up until the snap. Try not to pass always out of pass formations (like the shotgun) and try not to run always out of run formations (like the I formation).
Practice formations with both good pass and run plays, and get some runs working well. After you can run successfully against standard defenses, keep running to force the defense up and open up the pass. Then throw once they start bringing the safeties down to guard the run and the deeper stuff is open.
I also think it's better to pass about 50% on 1st down. It's easy to run on first to try and get a 2nd and 5, and then have a couple short down and distances for a first. However too many people always run on first down. This can be shut down by run-stopping on first down, then pass-defending the next two plays before a punt.
So try to mix up the run and pass. If you are bad at one or your team doesn't have good players for it, practice.