Encode AC3
Open up [b]Sound Sound Forge[/b] and open the .w64 file you created with eac3to. It will take a few minutes for the audio to be processed. Once completed, go through the audio and highlight a region in the Center channel (usually the third stream in 5.1 sources) that has primarily dialogue (no music or sound effects). Make sure to only select the center channel, otherwise all six channels will be averaged and you will get an inaccurate value. Then click Process->Normalize. Click the Average RMS level (loudness) radio button and then press Scan Levels.
After a few seconds, a value should show up for the RMS (undernearh the Scan Levels button). Write down/remember this value. Now click Cancel. Make sure to click Cancel and not OK, otherwise Sound Force will normalize the audio.
Now click File->Save As. Make sure "Dolby Digital AC-3 Pro" is selected and the "5.1 Surround DVD" profile is selected. Now click the Custom... button. On the first tab, make sure the settings match below. Change the "Audio coding mode" setting to match your audio, e.g., pick 2/0 for stereo audio. Also make sure the "Data rate" is set to your desired bitrate. Stereo audio is often encoded at 192kbps, and surround audio is often encoded at 448kbps for SD encodes and 640kbps for HD encodes. Then set the Dialog normalization to the value you wrote down earlier. (In some cases, the value you calculated before may be below -31 dB. In this case just choose -31 dB in the dialog.)
Now go to the Preprocessing tab. Uncheck all input filtering and surround channel processing. Make sure that RF overmodulation protection is unchecked. For the Line mode profile, the recommended value is "Film: Light".
Some people do not like the idea of compressing the dyanmic range of the audio, and will recommend choosing None for the Line mode profile. The concern is understandable, but in most cases encodes are going to be viewed on computer speakers or in an amateur home theater (especially considering this is an SD encode if you're using Sound Force). Having the full dynamic range is unnecessary and will make the film unpleasant to listen to if there are any loud/soft noises. The choice is ultimately yours. You can read this article for more information
Finally, press OK and then Save the .ac3 file to the folder of your choice.
The resulting file will be your final main audio to be used later on down the line in muxing.