The used matrices aren´t really normed and are based on trying by the authors from this page: http://www.3dtv.at/Knowhow/AnaglyphComparison_en.aspx
I also included the other matrizes from that page, just remove the commentmarkers in front of them and uncomment the currently used one. If you have really a lot of trouble to get anything working you should may try the matrices for real anaglyphs which should work without a problem as long as your display shows the colors right. When creating a 3D photograph you usually create the images from just a few centimeters shifted position without changing the angle. Though you can definatly improve the experience through playing around with the angle (I wanted this as easy as possible to use and got rid of it). When the pictures are combined and you look at them through some glasses, the layer without a offset will seem to be ad the screens position and then depending on which color is on which site, things will go into the display or come out of it.
The bigger the offset is, the deeper the scene will seem to be. But it will be hard to see 3D if the offset is bigger then the offset between your eyes (I often read 6cm for this). You should also play around with the views arc parameters.

When using color filters you will usually throw the red channel completely away.
The alternative which is often used is as BlueBeast already said are polarised glasses. But you won´t get it to work on a computer monitor easily. You have to use two beamers for this with different "filters" in front of their lense so the light will be different for both pictures. You also need a special projection surface which dosn´t manipulate the light (it has to mirror it very nicely) and then each glass in front of your eyes will let pass only the "fitting" light.

For computergames there are also shutter glasses which will always close one eye and change the image.

Some other nice practices for 3D is to learn crossview and parallelview (just search for it ) this will also make it a bit eaysier to look at anaglyphs with a quite big offset.

Since the cyan filter will often have also some red passing there can appear some ghosting, but you should usualy still see it in 3D if it isn´t too bad.

Just some experiences I made in the last weeks