Call me a rotary retard... I'm ok with that. I don't know which ports are the "5/6th ports"... I was looking at an intake manifold and comparing it with the 4port manifold, I assume either the top or bottom ones on the "outsides," are the primary and 5/6 ports... while the inner two are the auxillary ports? assuming this is true, which (top or bottom) are the 5th and 6th?

 

More properly called the aux ports, they are located above the secondary intake ports on the end irons. If you look at a 6 port manifold you will see that the outer ports are comprised of two circles. The top circles lead to the aux ports.

The inner two ports on all side port rotary engines are the primary ports. They are located on the center iron.

The outer irons house the secondary ports.

On 6 port engines, the secondary ports have an aux port above them.

 

This should help:
http://mazdarx7.iougs.com/intakeair.shtml

There are 3 sets of ports on a 6-port rotary: Primaries, secondaries & auxilliary ports. The primaries and secondaries are always open, but the aux ports are switched open at 3800 rpm via actuators and rotating sleeves.

 

just look at the LIM and there should be a rod sticking out of it that turs the ports open i think it should be the bottom.

 

You are on the right track. The top ones are the 5/6th ports, you can look at where the sleeves are in the intake manifold to giveaway the 5/6th ports or find a picture of an n/a iron and you will get it in a second.