These audio issues became more acute recently when I added a 2-meter transverter to my Flex 6300 and started using FM on a daily basis. Audio quality issues aren't quite as apparent with SSB as they are with FM, and in my case, it was a lack of audio amplitude from my Logitech USB headset through Windows 7, and too much echo from my alternative studio-quality USB desk mic (my new office has high vaulted ceilings, causing the echo chamber).
After much research and experimenting, I finally found a solution that works for me I'm sharing for others to benefit from as needed. The solution was to get a higher-quality headset with basic noise cancelling, and one with an adjustable mic that can bend around closer to the actual audio source (the mouth), coupled with some audio processing software for Windows. This combination addresses all three problems - audio amplitude, background noise and echos, so now my voice has the right level of punch for FM, AM and SSB modes.
I have a local ham who has been helping me adjust the audio levels. For me, +10 dB above Windows full audio input levels is about right to get full FM deviation without overmodulating. Interestingly, I no longer require the SmartSDR PROC setting to be on to get full amplitude punch. My guess is this will also improve my SSB P-P signal, as well. I will experiment next time there's a DX pileup with and without the PROC compression.
Here's the solution that works for me:
USB Headset: Mpow 071 USB Headset/3.5mm Computer Headset with Microphone Noise Cancelling, Lightweight PC Headset Wired Headphones, Business Headset for Skype, Webinar, Phone, Call Center
I'm sure there are other Windows software drivers and equalizer programs out there, but this solves the problem nicely. I'm not yet using the equalizer to further improve the audio quality, so there may yet be room for improvement.
Lastly, in order to test my audio without the Flex radio on a standalone basis, I downloaded the nice audio editing software "Audacity", which let's me record and play back high quality audio and see the waveforms visually on the PC with no further test equipment.
So as usual, I'm finding the flexibility of being "software-defined" has its benefits!