If you want you can use Profiles and have this all preset to use different antennas on anything from Bands to Modes of operation. There is no need in this case for 3rd party programing SDR handles this well.
There is even a dedicated receive only position which I use when 40 thru 160 are noisy.
Typically the default antenna 1 but you can program it to be anything.
Not even quite that simple. As George said there are 5 receive sources.
Also, for the 6700 there are 2 SCU (Spectral Capture Units) or AtoD converters.
RULE 1: A SCU may ONLY be connected to one receive antenna at a time HOWEVER both SCUs may be connected to the SAME antenna for receive.
For the first 2 panadapters (any letter combination) they may be assigned to ANY receive antenna. If you choose two different antennas the panadapters will, by software and relay switching, also be connected to different SCUs (Rule 1 with 2 SCUs)
For the remaining 6 panadapters, software will connect to EITHER SCU PROVIDING that SCU is connected to the requested antenna. If NEITHER SCU has THAT antenna the SCU/panadapter pair WILL BE changed to the requested antenna and the previous panadapter (of the first 2) will SWITCH to that antenna as well. (Rule 1 - 1 antenna per SCU). Note it the first two were on the same antenna then one SCU will service the first 2 panadapters and the other SCU will switch to the requested antenna and service the new panadapter.
Confused yet? Quite the logic inside the radio.
Common question, especially on 6300/6500 with 1 SCU is why when I change the antenna on panadapter x does panadapter y change antenna. Answer: 1 SCU and 2 antenna selections - something must change.
6700 Variant: I start a 2M panadapter why does my 20M loose its antenna? Answer: You also had a 40M panadapter open with a different antenna; something had to give way to 2M XVTR
Let me be more specific...
Pan A is on 40 and using the 40 antenna on ANT1
Pan B is on 20 and on the 20 antenna using ANT1
When I open Pan C on 80 meters A remains the same and same antenna, B remains the same on the same 20 meter antenna..
C is receiving FB on 80 but I have no idea which antenna it is using but not the 80 meter antenna and it is also set to ANT1.....Ant1 is the only port on the flag that works.. all the others seem tobe not connected.... My Antenna Genius has an 80 meter antenna but the 6700 just uses the 40 and 20 meter antennas....so who is on third??? Beats me hi hi
Antenna Genius - then you have the 6700 ANT1 connected to it, also ANT2. Then the antenna genius switches which physical antenna is presented on what you are calling ANT1.
From your description, the 6700's view, all 3 panadapters are on ANT1 and the AG switches according to (personally) unknown criteria.
As George suggested, connect 40M to 6700 ANT1 physical connector, 20M to 6700 ANT2 connector, and 80M to any of RXA/RXB/XVTR and experiment. You will see the panadapter antenna selection change as they are added. Experiment until my Rule 1 makes sense.
Then complicate things with the AG.
Other members? - Please explain how the AG functions in this environment with 3 antennas connected through 2 switched ports, to a dual SCU 6700 and only 1 panadapter with TX red indicator lit.