You’ll probably be a lot happier using PeerGuardian 2. It works for all applications, not just those that recognize a filter file; updates itself rather than requiring you to remember to do it; doesn’t need a long time to process and integrate various blocklists; and doesn’t require you to export files all over the disk so the various applications can find them.
It’s very difficult to understand your post, but there are a couple of points that I think I do comprehend.
PeerGuardian should be used instead of, not as a supplement to, ipfilter.dat
It’s been my understanding that a subsequent rule overrides an previous rule if there is a conflict, in ipfilters generally, so if your first and second rules say “allow this, allow that” and your third rule says “allow nothing” then the third rule wins and nothing is allowed. Make your restrictions first, followed by your permissions rules and it should work the way you want. I’ve never encountered any filter that works as you describe, “process the first line or first two lines then stop”.