Pairing must be made manually using the BT manager in BlueTools 1.00. But pairing is seldom necessary to connect and use a GPS device.
About COM-port number. When your application act as a BT serial client (using BlueTools) it is up to you what you want to do with the data coming in and out. You could for example create a virtual port yourself using SerialTools Pro. But there is no COM-port automatically "assigned".
Note that you act on a BlueTooth service level. One way of making a BT serial port service available to legacy applications is through a virtual port. But if your application is the only user of the GPS data, you should simply don't care about any COM ports, you simply read and write data directly to the GPS using BlueTools.