Well if the two colors have been recorded right after each other you could just append the 2nd color to the first list, offset the frame number and run the drift correction. This can be even done in programs like Excel.
If there is a time gap you would need to calculate the corresponding frame for the events of the 2nd color.
If you are familiar with MATLAB or something similar - you can work on the raw localizations to align them. I use this built-in function: http://de.mathworks.com/help/vision/ref/pcregrigid.html
which gives me good results (even without fiducials - depending on your structure of course)
For 2-color-visualization I either use FIJI and just load the two separate super-resolution images (after the aforementioned drift correction) - combine them into a stack and assign the colors to them. Or I just use a standard image editing software (like photoshop, gimp, ...). I find it too cumbersome to do that in MATLAB and fiddle around in the RGB space.
Philip Gröger (BCUBE, Dresden)