These instructions assume you have calibrated and aligned your Red, Green, and Blue images. If you have not, follow the instructions on how to calibrate and align your images using AstroImageJ.
Open each of your images individually (i.e. do NOT import -> Image Sequence) by going to File -> Open. For each image, go to Scale -> Full Dynamic Range. Go to one of your images, then select Color -> RGB composer. This takes a second to load, and a new "RGB-composed" image should open, along with a red, green, and blue RGB composer window. Check that your red, green, and blue images are in the right order in the RGB composer window, and then adjust the lower and upper bounds of each channel to 0 and 255 (this worked the first time when I used SkyNet images, but with an image of M27 from the Observatory, I manually adjusted the channels), respectively, and hit update for each to see the changes. This should produce a rough, correctly colored image. You can keep adjusting the channels in AstroImageJ, or you save the image by going to File-> save as TIFF, which will be an uncompressed image that you can open in Adobe Lightroom or Photoshop to have better control over in post-processing. For natural looking images, adjust the colors to produce a grey backround (~20 for red, green, and blue). Happy Hunting!