You can use whatever com port on the pc that you want. It's rare to find more than one these days but they should be labeled.
Hyperterminal does not know or care what you should type after connecting. That's going to be documented in your manual. It might say that in order to perform such and such an operation, you need to enter the string A1. Type that and hit the enter key.
There are two basic types of serial cables. A null modem swaps the tx and rx lines. That means that the tx pin on the pc is connected to the rx pin of the instrument and the rx pin of the pc is connected to the tx pin of the pc. If the cable is not labeled, use an ohmeter and check for continuity. Stick one of the probes on pin 2 of one of the ends and stick a probe on pin 3 of the other end.