iPod A/V encoding question

[Chainmax]

I'm going to make a test encode of a Simpsons short from my 1st Season DVDs. The video will be encoded with MeGUI using the iPod profile and the audio will be encoded using the Nero Digital Audio encoder. Once I have the two files (an .mp4 and an m4a respectively, right?), what container should I mux them into? Also, after the muxing do I only need iTunes to upload the video to the iPod?

[check]

You should mux with mp4box (ie the muxer that the meGUI mp4 muxer uses).

Also, make sure the audio is only LC-AAC. If you are using quality mode, you need to keep the quality above 0.3. For adaptive bitrate, I'm not positive, but I think the limit is above 64kbits.

You can add the video to itunes and it will then sync with the rest of your music

[Chainmax]

I didn't know audio had to be LC-AAC, thanks for the heads up. I'll be using -q 0.35 so it won't be an issue (HE-AAC starts at 0.301).