The AFT/PFT during Basic don't "count" as part of your Physical Education Average. However, if you score low enough on one or both of the tests, you can be placed into an academic year program run by the Recondo people (since you don't technically have a PEA, you can't technically be on athletic probation, but they will suck up plenty of your time just as if you were on it.) It's basically a preventative measure to make sure that you don't start with extremely low scores by the time you take your first semester AFT/PFT.
If you can't do a pullup, you won't automatically fail the PFT, I know plenty of people who have struggled with them and still have easily passed every PFT. Same with the jump, so the best advice I can give is to spend some time trying to max the other sections while you target whatever event(s) you struggle with. There's more than enough advice out there for improving PFT scores but if you'd like some more (particularly on going from sucking at pullups to maxing the section), PM me and I can help out.