The PRT Standard has changed three times since I've been in the Navy. Currently, there are 4 levels (sat, good, excellent, outstanding) with three sublevels each (low, med, high) For each event, you get a score from 45 (satisfactory low) to 100 points (outstanding high). EXAMPLE: Excellent Med on pushups and situps is 80 points each, good low on the run would be 60 points. Your overall score is the average (80+80+60)/3=67 or Good Medium. BUT you must pass all sections to get a passing score. Simple answer, do your best on push ups and sit ups, but make sure you pass the run, also.
As far as the in PRT/ out PRT question, do as well as you can without hurting yourself, and make sure you'll be able to do as well on the out PRT, regressing never looks good.