If both ports go to one side of the diaphram, you need to cap one off. I'm assuming if you blow into one of the ports, air would just blow out of the other one. I don't know what that turbo is stock for, but most likely the second port went up to a boost controller that would bleed off pressure to controll boost. The two ports on the turbo may have just gone to different areas on the engine, one to the waste gate, and the other to a sensor, possibly tied in with the boost controller, who knows. Shouldn't really matter if you use the large or small port. Whatever one is left just cap, and the same goes for the port on the turbo, unless you want to run a seperate line up to a boost gauge, or whatever.
Jason
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