doomleox999,
as an alternative you could try downmixing and encoding with foobar2000. I use it for 99.9% of my audio encoding. You can add DSPs to both the playback and conversion chains and conversion configurations can be saved as presets. There's plugins for decoding audio it can't decode "out of the box" (DTS and AC3 are the main examples) and there's even a plugin for decoding Avisynth scripts.
Not that I downmix much these days, but if I downmix and encode a bunch of related files (episodes of a TV show etc) I usually downmix with the
matrix mixer DSP while reducing the over-all volume by 6dB. It's not quite enough to guarantee there won't be clipping, but it's enough most of the time, and that way the relative volumes of each track doesn't change. Once it's encoded, I run a ReplayGain scan on the encoded audio to check the peak levels (I encode with either QAAC or ffmpeg's MP3 encoder so the peaks aren't clipped before encoding). If a track or two has peaks above 0dB I'd probably re-encode them with a limiter DSP in the conversion chain. On the rare occasion there's lots of tracks with peaks above 0dB, I'd decrease the volume of each output file by an appropriate amount (so the relative volumes remain the same). Foobar2000 can losslessly adjust the volume of MP3 and AAC audio in an MP4 or MKV container, or alternatively you could reduce the downmix volume and re-encode them all a second time, which isn't as bad as it sounds as you can encode multiple files simultaneously.
Fb2k comes with it's own downmix DSP but it's not configurable and it doesn't reduce the volume to prevent clipping.
There's a screenshot of the matrix mixer DSP below. The coefficients are specified as a percentage, as they are when downmixing with Avisynth or ffmpeg. This is my standard 5.1ch to stereo downmix preset with an overall 6dB volume reduction. Both the back and side channels need to be included for 5.1ch, as the surround channels can be in either the back or side.
