how to shoot for 3D?
 

So I have 2 HDR-FX1 cameras, and I'd like to build a base to put them together. The 2 videos will then be put into after effects to combine into the red and green "3D" video.
Is there any standard way to build this, or any thoughts on wether or not this is the right approach?

This works but the wide interaxial distance between such large cameras will have an impact on how close you can photograph your subjects.

Watch this little CNN piece on the basics of 3D to see one such rig using Sony cams.
Secrets of the Magic Eye

dont use AE and dont create anaglyph video, because color compression distort the good 3d effect.
instead, render the two stream separatly, and use the free stereoscopic player to play real time in the format you want!

Stereoscopic Filming
 

Yes these 2 HDR-FX1 are far to big to use in a side by side system, the lenses can only really be 75mm or less apart, so not much bigger than the separation of human eyes, so if you must use these cameras for 3D then you are best to use a semi silvered mirror with the cameras at 45 degree angles to the mirror that is also at a 45 degree angle. This enables your lenses to be almost on top of each other and gives much more flexibility in stereo shooting, the downside is it can be rather bulky.
As far as after effects goes, the advice about stereoscopic player is good advice, always keep your stereo material separate for archive purposes. You never know what new ways are around the corner for displaying 3D, what you don't want is to make your 3D masterpiece and end up with only an anaglyph master, always go for side by side format and then you can make any 3D format from that master. A word on anaglyph, please do not use Red/Green anaglyph, it’s better nowadays to use Red/Cyan for better anaglyph results.