I can tell you this: keep HIPS on safe mode or untrusted; pop-ups allowed. If you put it on heightened alert it will drive you nuts. The only flaw I have seen in CIS is that I was ignored often when I attempted to whitelist when HIPS was freaking out.
I think I used to keep the BB and auto-sandbox on "untrusted" and allow the BB to notify you with pop-ups. If you prevent notification via pop-up, then you are forced to allow all, or disallow all, if I remember right, and neither one of those are acceptable, in my opinion. You can play around with it a bit. It won't bite.