TDA3 or TAW4/5? Because 4/5 is a big improvement. The menus are actually somewhat decent now! Worth a look.
You can split the original audio file (AAC?) with YAMB. But it's still AAC, not AC3. So you'd need something else to convert. This all-in-one solution, for once, sounds helpful. Just watch so the bitrate is good -- at least 256k, if not 384k. You don't want some medium-quality 192k or 224k AC3, especially if the source has any noise in it (hiss, etc). Noise causes the medium compression to be low-quality compression!
A good cheat is to use Adobe Premiere Pro for the audio streams. You can see the waveforms, unlike Womble. I wish Womble had the audio visually. You can then export the audio only as WAV from Premiere (or use AME to export as AC3, MP2, etc). You only need Womble if editing the MPEG (non-reencoding, unlike Premiere). You're usually editing one or the other, not both.
You may also like Womble MPEG Video Wizard more than MPEG-VCR. I do.
Can't wait to see the finished project.