Hey Abuantenna,
You were right when you said you just draw a rectangle and assign a waveport to it. Just be dure to define the integration line from the CPW to the ground plane. Obviously, the port is going to be perpendicular to the plane of the CPW and you know the approximate sizes of the edges of the port.
I had another suggestion. Before you hit the analyze button for the whole structure, do simulate the ports first and see if the port impedances are what you need in your structure.
I've never used CST and hence wouldn't know what you're talking about!
Ananth.