Smile [Q] Custom ROM and GravityBox fighting over control

I have flashed Paranoid Android on my Nexus 4 after getting tired of stock upgrade OTA messages and failure to apply them. The ROM works just fine but it seems GravityBox has lost some of its gravity. It turns out the ROM keeps changing things back. Is there a way for them to make peace? I pretty much need the following pieces:
  1. customized battery icon. I love the ring with percentage style but PA keeps changing it back.
  2. control over quick settings. with GravityBox I can simply change size, rearrange. I turned it off in PA. but I want it back.
  3. more control over pie. The best I have tasted is Pie Control. The one that comes with PA doesn't work as well.

Also I think there used to be an app dedicated to PA settings. I can't seem to find it any more. Is it obsolete? How do I control the behavior of PA built in features such as immerse mode show status bar or not, show pie or not, etc.