You HAVE to put two GP-49's into the main CP, if you're going to use two 49-ways in it, so that part is kind of dictated by the design.
Where I would differ with some of the previous suggestions is that I would build an interface BOX for the second controller, using either a KeyWiz, an I-pac, or a GP-Wiz.
What I'm thinking here is to have the actual wires from the 2nd CP terminate in a 25/36/50-pin connector that could plug directly into a corresponding jack on the first CP, and use the interface inside that CP for 4-p operation.
The two GP-49's give you more than enough extra inputs to piggy-back the second controller onto the first without having any of the reconfiguration issues inherent in the multiple interface scenarios above.
When you want to use the 2nd CP as a standalone, you would just plug the cord into a box that has a Key-Wiz, I-pac, or GP-Wiz inside, and then connect the PS/2 or USB cable coming out of that interface box to whatever computer you like.
This is basically the configuration I am currently using on a bunch of my "test" CPs, although I am using an AKI, SJC, and an Oscar Mouse Hack while doing it.
If you are swapping interfaces around, you will probably have reconfiguration issues.
If the interfaces stay connected, and just the controllers swap in/out, you will not have those problems.