I’ve tried many third party apps.
Many free ones?
You got lucky. Audacity will typically refuse to work with a second sound program running at the same time. You have two. That makes you a unicorn like Chase who used to run the Reel-Life podcast on one PC with Audacity, Skype and no other special considerations. He’s looking at the rest of us wondering that the fuss is all about. He is a unicorn. Nobody else can do that.
I do this with a stand-alone sound system and its own volume control. When I get a call or there’s somebody at the door, I reach over to that big black knob instead of trying to hit the right keyboard keys multiple times or mousing to the [- speaker] icon.
I do the whole podcast/Skype thing with two computers and a mixer.
That’s how the big kids do it, too. You’re pretty much stuck with that if you expand. My headphone volume is on the mixer.
We recommend Pamela paid software. Pamela “knows” about Skype and will record high quality stereo WAV files with you on one side and the far side on the other, suitable for editing, filtering and post production in Audacity.
http://www.pamela.biz/en/products/
There are other products too (in case you missed some).
To bring this around, no I don’t think there is a way to adjust that now that you have all the sound pathways tied up. That’s one of the shortcomings of Stereo-Mix. You might find something in our tutorials for internet recording.
http://manual.audacityteam.org/man/tutorial_recording_computer_playback_on_windows.html
Koz