Hi Morgan
PixInsight LE currently hasn't included any process to help you in the aligning (register) task. You have to do it in other softwares, or suffer the pain of "manually" rotating, shifting, scaling, etc. with the geometric transformations avalaible. We are working on a fully automated tool for the PixInsight Standard release (that will be comercial). Right now we can automatically align images that are not very different, like series of images for combining, but the tool has to be improvement to allow mosaic composition and registering images with large scale differences.
Well, if you have your color filtered images previously registered, and they match exactly (same size, too), you'll need to use the ImportChannels and optionally the PixelMath processes.
First, convert one of your grayscale images into a RGB color one (Image>Color Spaces> Convert to RGB). After that open the ImportChannels window, and select this new RGB image as the target. Select the RGB color space and disable the auto identifiers checkbox. Now search in the lists for the propper images, and disable the channel that you used for the "background". Finally, if you want to change the weight of the channels, use PixelMath, just changing the weight of the result's individual channels and apply it.
For more in deep info read the documentation chapters of Import/Extract Channels and PixelMath (see the examples).
