After Effects :: Multiple Audio Tracks In One Video File Import?

Mar 29, 2014

I'm trying to get back into making youtube videos and I am running into an issue. I have an Hauppauge HD PVR 2 gaming edition. Now one of the features that makes it easier for commentators like me is the ability to have all of the audio channels [game, mic, PC (aka skype chat)] all on seperate "layers" that way you can go into your video/audio editor and have the different audios so you can tweak them individually.
 
The problem that I have and wondering about is this, is there a way to import the files and have the different audio tracks be seperate? The files that they come in are either .ts [raw] or .mp4 [in program compression]. I would like to keep it in .ts even though its a bigger file as I like my compression style after I've edited that gives the best look without loss when uploading to youtube.
 
I have see the free program at any-video-converter.com mentioned, but the issue is last time I used it I somehow ended up with a virus. I also have handbrake, the Master collection cs 5.5, and VLC.

Operating System: Windows 7
Software Version: 10.5.0.253
Device: HD PVR 2 gaming edition

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