No, positive air pressure means essentially more air is entering than exiting.
If you have "holes" it will create negative air pressure, if anything.
this isn't true either...
PAP and NAP can only be achieved in a fairly well sealed case, where the only places air can enter and exit the case are through the intake and exhaust fans/ducts, and nowhere else. it doesn't matter whether intake CFM > exhaust CFM (PAP) or intake CFM < exhaust CFM (NAP)...if there are uncovered holes elsewhere in the case, any positive or negative pressure that might otherwise be induced by the arrangement of case fans will be negated by those holes. open a hole in the case of a PAP system, and air will flow
out of the case through that hole until the pressure inside is equal to the atmospheric pressure outside the case. open a hole in the case of a NAP system, and air will flow
into the case through that hole - again - until the pressure inside is equal to the atmospheric pressure outside the case. so leaving the holes open in his case prevents the OP from achieving either a positive
or a negative air pressure setup.
that being said, i agree with you on your other point - the OP should cover the holes and see what happens...
ideally, the experiment should go something like this:
1) cover the holes, either with plates that do a fairly decent job of sealing them off, or with additional 120mm fans (since that's what those holes were designed for in the first place).
2) play around with several different fan configurations using 2, 3, and 4-fan configurations.
3) either one of the PAP scenarios, one of the NAP scenarios, or one of the unpressurized scenarios will hopefully win out for best airflow and lowest temps. or perhaps you might find that 2 or 3 different configurations all hit the same low temperature that the other configurations couldn't hit.
this may seem like overkill considering you're not having problems with overheating...but you did mention wanting to get the best out of what you've got, and this is the only way you're going to get there.