Maddy

At this time, StereoMovie Maker does not have a Hue adjustment filter or a Channel Mixer filter, so you can’t optimize anaglyphs by using just StereoMovie Maker. Hopefully, Masuji will someday add this ability (as in StereoPhoto Maker).
However…
You can optimize and tweak anaglyphs, using identical methods as I used in my other anaglyph optimization tutorials, by using VirtualDub for the first couple of steps, frameserving to the AviSynth script (just as in the VirtualDub tutorial), then opening the script in StereoMovie Maker instead of a third application of VirtualDub. This way, you are able to use the stereoscopic alignment tools in StereoMovie Maker, if you prefer (but there are also VirtualDub filters that will work for alignment, too).
Just follow the VirtualDub tutorial, then open the AviSynth script in StereoMovie Maker:
http://www.puppetkites.net/blog/archives/92
Assuming you use VirtualDub for the Hue adjustments and the Channer Mixer settings (which is the whole point of my anaglyph optimization method), be sure to use the standard anaglyph conversion in StereoMovie Maker (Stereo > Color anaglyph > Red/Cyan), i.e. don’t use a Half Color conversion or something other than the standard red/cyan conversion… all the optimizing is done in VirtualDub.

Have fun!