Only one application can use a particular COMM port at a time.
Unless they both have some sort of "disconnect" or "close port" feature, you'll have to shut down one application in order for the other to communicate. If they both can open and close the port with menu commands, you can close the port with one and then open the port with the other. The application with the closed port will not be able to communicate until it opens the port again, but you can still have the program running and use whatever "offline" features is supports.
Multiple COMM ports can be used simultaneously. If you are trying to talk to two different devices, you could buy another COMM port.
If the data is one way, i.e. just coming in to the computer, then you can use a program called Franson GpsGate to share the data stream among many applications. I've used it successfully with GPSs and other "one-way" serial devices.