There's no real advantage to using the Media Encoder. The files will look the same.
As long as your project settings match your video source, those output settings should give you excellent quality on YouTube. About the best possible, in fact.
It doesn't matter whether you use MP4s or FLV files.YouTube will still YouTube-ify it.
Thanks for the reply. Ok, I'll stick with those settings. However, one question: there's no option for choosing 256kbps for the audio (just AAC). If it's choosing 128kbps or 192kbps AAC by default, wouldn't being able to select a higher bitrate audio (such as 256) provide better quality? (since these are music videos, I'm trying to get the best audio possible from the DVD).
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I doubt that even a discerning ear to tell the original source Audio, after YouTube gets through Transcoding it for display. Also, viewers will be listening through their computer's speakers, and not a full home theater setup, where the Bit-Rate might make a slight difference. Also, most folk today, think that MP3's through ear-buds are "high fidelity."
The only plus for using AME is that once you have queued the Project up, you can do other things, while it is processing the file.