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Ok, my processing chops arnt great, I'm still learning as well but I have the same gear and filter as you do and heres what I've found.
First of are you shooting in Raw yet, i recall you were shooting in jpeg before?? If you are, you can tame that blue tone by reseting your white balance in the canon photo professional.
Double click on the image you want to edit then right click/tools then there are three tabs up the top of the tools window select raw. Youll see a button that say "Tune" click on that and you see the "White balance fine adjustment" box come up. Click anywhere on the circle and you will see the picture change in colour. Select a spot that looks best, right click and save the ricipe to the clip board and then hight light all the images that you are going to stack, right click on one of images the and paste the recipe file/apply to all images. This will set the white balance the same for all the images. You can also go into to the rgb tab and aligne all the colours but i think most people do that in photo shop. Do you have photo shop? Your going to have to get something like it because there is only so much that you can do in the canon app.
Now open your stacking soft ware and stack. You'll probably still get a very pale cast over the image, you can fix this in photo shop with "Levels" or if you are using the canon app you'll need to use brightness and contrast in either the raw or rgb page in the tool palate. You can do a decent job with just the canon app, at least to noob eyes anyway.
Anyway thats a place to start from, hope it helps.
Sandy
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