Importing a Video with 2 audio tracks

I think your friend is confusing the way AE treats a file with a stero pair (left and right) vs how it treats a file with multiple tracks of audio.

After Effects is not designed to be a video editing app; it is designed to create visual effects, composites, motion graphics, and animations that can be edited in an NLE like Premiere Pro. Most of your compositions should be one shot that is rendered to a visually lossless production master and edited into a movie using an NLE. More than 50% of my work is for dramatic films, and the other 40% is corporate and industrial mixed with commercials. Almost all of my comps are less than 7 seconds. About the only MP4's I render directly from After Effects are test renders of shots to send to the client for approval. If you are using AE to edit gameplay videos to share with others, you are walking into a dead-end street. Stick with Premiere Pro for editing and only use AE when you need to do something to a shot that you can't do in Premiere Pro. It will save you days and days of frustration.

The friend that said he could import video with multiple tracks is mistaken. Premiere Pro or any other NLE is the first choice if you need to manipulate multiple tracks. For further refinement, use Audition. You can go from Premiere Pro to Audition and back in a couple of clicks. 

Mylenium is quite correct, of course.  AE can't deal with multitrack audio.  Just drop your file into a Premiere sequence, solo Track 2 and export a WAV file.  Now import your original MP4 clip and the wav file into AE and place them together into your comp.  The MP4 clip will play Track 1, and the WAV file will play Track 2.

Of course, AE is a terrible place to mix and edit audio. You'd find it much easier to work with doing it in Premiere.

The duplicate sound is just AE trying to fill the "empty" track the Premiere tells it is there because it can't access the otehr channels. Sort of a glitch, if you will. That doesn't change the overall facts, though. You can't have embedded multitrack audio in AE. All additional sounds have to exist as separate files/ layers.

Mylenium

Your freind is wrong. It's perfectly normal. AE can handle exactly two audio channels per file and that's it. If you plan on using multiple tracks you have to extract them in Audition or Premiere and import them as separate audio files.

Mylenium