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Normally you should use GoPro original app (GoPro Studio) but since it works ONLY with synced via original orange cable footage you will not be able to get automatic sync, and this way is closed for us. So i use Adobe After Effects for syncing and color correction. Basically all you should do is to drop both footages (left and right) on a timeline, find some noticeable audio-peak on both audio tracks and align them as close as you can (minor shift in frame or half frame is ok, and i never saw 100% alignment )) )
After you align footage on timeline clip both clips and do what you want (i.e. cut, color-correct, etc.)
Important things not to miss:
1) while shooting - clap your hands 2-3 times near the camera - you will get nice noticeable audio peaks at the start
2) try not to swap left and right footage )) - or you will get strange headache while watching it on a TV ))