Encoding Bluray with x264: P3 - Audio Encoding

Now we will encode the audio.

Open TsMuxer.
Click add and select the same .m2ts file we used in Avisynth.

Select the files we wish to demux. We can uncheck the video as we already have it encoded.
For TrueHD+AC3 audio files in our particular package, down-convert them into AC3. MeGUI doesn't support demuxed TrueHD files as of this writing. [Edit: Eac3to supports TrueHD]. For all formats, we can leave them as is.
Remember to set the Output to demux and our output files to our predesignated folder. Also note, which the audio track number and which language it corresponds to (track=4352, lang=eng / track=4353, lang=jpn) Start demuxing and when it is complete, we can check the output folder for our files.

Return to MeGUI
Under the Input tab in the Audio section, right click Track 1 and select New Track because we have dual audio.

Next, select the audio inputs for each track. In encoder settings, select Flac and Config. In the following dialogue box, set the preferred audio decoder to FFAudioSource. Finally, select the Compression Level to smallest file size.

Finally update *scratchpad* or create a new profile.
When we return to the MeGUI window, queue each track.

Click the Queue tab. We will see all the files we have queued, including our video track. Select the video track, then click start. Do not send each file to different workers and run them simultaneously. Remember that the computer will be reading the same .m2ts file on the HDD.
When after one job is complete, MeGUI will automatically begin the next, so our work here is now done.