Hi Jeremy,
Here is a manual method to do it & use Ha as luminance too.
With a manual method you can see what's going on.
This method is quite good because it will almost automatically assign the grayscale images to RGB.
Obviously you need to work on each file with stretching, levels & star masks first before combining but here goes:
Open the 3 RGB files :stack of red , stack of green , stack of blue.
Click on the red file.
Click on channels in the layers window.
Click on the right hand side down arrow button.
Click merge channels.
Change mode to RGB inside the little box that pops up.
Click OK
For Red select: stack of red
For Green select: stack of green
For Blue select: stack of blue
Click OK
Go back to layers inside the layers box.
Save this RGB file in case you need it again.
Open the luminance file called stack of luminance.
Stretch it using a star mask to protect the bright stars.
See here for star mask link:
http://www.youtube.com/watch?v=UZlpDFsugYk
Go Ctrl A, Ctrl C to copy it.
Click on layers of the RGB file above & go Ctrl V to paste it as a new layer
on top of the RGB. ( Rename it Luminosity if you want to )
Set the blend mode to luminosity.
Now - open the Ha file called stack of Ha.
Go Ctrl A Ctrl C &
click on the now RGB L image & go Ctrl V to paste it as a new layer.
( Rename the layer Ha if you want to )
You should now have 3 layers in your layers window:
Ha, luminosity & RGB (if you have called them that )
now change the opacity of the Ha & Luminosity layers to taste.
The Ha can also be used as a luminosity layer just for fun to see what happens.
Note that if luminance & Ha is a bit noisy keep the opacity down.
Also remember to use Fitswork4 or some other program to fix any gradient problem.