The Setup command displays the GPS Setup dialog (pictured below). The GPS Setup dialog allows you to tell Global Mapper what port your GPS device is connected to your computer on and what format the GPS device is communicating in. Make sure that you have your GPS device set to NMEA-0183 v2.x or Garmin mode. There is also an Auto-Detect option which will cause Global Mapper to try and automatically determine your GPS device's settings when you start tracking the device. You can also specify that you would like to read GPS information from a text file containing NMEA-0183 sentences. The Data Logging section allows you to setup logging of the incoming GPS information to new text files. You can choose to log decoded position information (including latitude and longitude, elevation/depth, speed, heading, and time) in addition to raw NMEA data strings for connected NMEA GPS devices.
ADVANCED USERS ONLY: By default GPS serial connections use 8-bit, no parity, and 1 stop bit (8N1), but if you have one of the rare units that uses 7-bit rather than 8-bit data streams, there is a way to set that. You need to run 'regedit' and create a DWORD key named 'HKEY_CURRENT_USER\Software\Global Mapper\GPS_ByteSize' with a value of 7 (do this with Global Mapper closed), then your serial connections will use 7-bit mode rather than 8-bit mode.