Selective audio capture in games?

[Duke23]

I've been trying to use Shadowplay to capture my KSP activity lately for several reasons... Mainly the "shadow time" itself because there have been so many times I wish I could back up just a few seconds and hit record to get those unplanned awesome (or horrible) moments! But also because it's much less catastrophic on my framerate than FRAPS and provides smaller file sizes. My question isn't necessarily Shadowplay specific and I already expect that it's going to be a no, but what's the harm in asking?

So lately I've been watching Netflix some on my secondary monitor while I play because I'm apparently just not content doing only one thing at a time, and obviously it captures the audio in the background. Sometimes I like to upload to YouTube -- #1 I'm not sure how YouTube would feel about 'copyrighted audio' being in the background of my vids, and #2 I really don't want it there in the first place. I could mute the entire vid since KSP really only has some spacey music and engine noises anyway, but that isn't really the case with other games. I was wondering if there's another option. Is there a third party program or a reasonable method I can use to "hide" the audio from Netflix (or anything really) to keep it out of my recordings but still listen to it all at once? I feel like it wouldn't be incredibly difficult to do this on Windows 7 since the volume mixer already has separate channels for each application running and I've had to set up a virtual loopback device before, but I'm not making the connection here. It seems like there should be a way to make Shadowplay or FRAPS only record audio from one of those sources instead of everything that flows out of my audio jack. Any ideas?