You can do that, but personally, I would not recommend it and here is why. CP has an sk (cant recall the number now, but if you search app control best practices, it will come up) where it says best is to have any any allow at the bottom of the rulebase. In my opinion, thats just not smart at all...because, in reality, if your app control is say ordered layer, instead of inline, then EVERYTHING will get accepted, even if supposed to be dropped in access layer.
Here is what I did with one customer and it works amazing. We simply created section on the top of the rulebase with geo, app control and url filtering and beneath that, we set up bunch of inline layers and no issues at all.
I cant say that would work 100% for you, but I dont see why not.