It is kind of hard to give specific instructions because it is very different depending on the device and software used.

Q)Once I pair devices I need to establish a com port?
A)Yes

Q)Then there is also on the 6800 a port for "external gps" which has an option for com port and also hardware port.
A)I honestly don't know what this part is? Where abouts do you find this setting? It may be that you put in here whatever com port you selected and this is then set as being a GPS receiver. Without a 6800 though this is just speculation on my part I'm afraid.

Q)Then each program asks you which port?
A) Yes, normally in the program it will ask you which device to use for GPS, select the com port that you connected the GPS unit to.

Q)Also, what about the seeting where it asks me to manage the gps settings automatically (under the acces tab of external gps)?
A) Again I'm afraid I do not know. I have not had chance to look at a 6800 so do not know how it works or how it handles bluetooth/GPS connections.
What happens if you change to manually setup the settings for GPS? (if you can)