Well I can't say that I have any idea how you would configure any of this through a GUI, let alone GNOME's interface. But you can certainly use a Bluetooth GPS receiver. You need to setup RFCOMM, which essentially gives you a virtual serial port over BT. Once this is done, the GPS device would work just like the wired one you used previously.
To set the default PIN on your machine, you would edit the file "/etc/bluetooth/hcid.conf". Look for a line that says "passkey:" and change whatever is there to "1234".
Then you would find the device's BT MAC (assuming you don't already know it). For this you just run "hcitool scan" when the device is in discoverable mode.
To setup a permanent RFCOMM connection you need to edit the file "/etc/bluetooth/rfcomm.conf". You would edit it something like this (the only thing you would really need to add would be the BT MAC):
# RFCOMM configuration file.
# Automatically bind the device at startup
# Bluetooth address of the device
# RFCOMM channel for the connection
# Description of the connection
comment "Bluetooth GPS Receiver";
At this point you need to restart BlueZ. You didn't say which distribution you were using so I couldn't say specifically how to restart the service in your case; so you could simply reboot.
After that you should just need to enable the RFCOMM link with a command like:
sudo rfcomm bind /dev/rfcomm0 aa:bb:cc:dd:ee:ff
This will bind the BT GPS to the device /dev/rfcomm0, which you can then give to your GPS software as if it was a USB or serial GPS receiver. The software shouldn't need to know anything more than that, as it will appear as a normal serial port.
This all assumes you are using BlueZ 3.x, which is still the standard. If your distribution has switched over to the newer and less supported BlueZ 4.x, then disregard basically everything I just said. Then hope somebody has used a GPS under BlueZ 4.x and can walk you through it, because it is much harder to work with than the 3.x series.