Check out Chris Keller's awesome stereoscopic scripts for After Effects. The scripts are built to help you manage a stereoscopic camera rig in AE and preview your work inside After Effects with anaglyph glasses. The workflow is still a bit clunky because of AE's limitations, but these scripts are an incredibly well thought-out workaround for this, and they will save you hours and hours of work.
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If you want a simple method for YouTube (which automatically converts your uploaded video into different 3D formats and is probably the best way to deliver most projects), here it is. If you want a professional solution, you can ignore this.
First, record with two cameras side by side. They should be spaced about as far apart as human eyes, although you can push the spacing a little if you want a dramatic effect (and plan not to have anything too close to the camera). Capture and sync your footage in your editing programme of choice, then import into AE. Add your footage (left and right camera) to a comp with dimensions that match the footage. Then reduce the scale of the two footage items so that they are 100% height and 50% width. Position the right eye footage on the left of the comp and the left eye footage on the right. Because the footage items are 50% of their normal width, the entire frame should now be filled.
Export the comp and upload to YT. Be sure to use the following tags: yt3d:enable=true yt3d:aspect=2:1
The first tag tells YT that this is a 3D video, which enables the 3D controls. The seconds tells YT that your video has been squashed to 50% width, and this will ensure it is scaled back to normal size.