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While it is possible to do in Photoshop, I have always used DSS as it is so easy and gives perfect registration. Once you have each of your filter subs registered in DSS, you simply create a Group of your three final filter images and register those together. This will align them, and produce three registered files and you don't need to save a composite, just take the registered files into Photoshop. You need to tick the box in the DSS file tab to save the reg files to your directory, but it is an easy automatic way to do it.
When you open the files in Photoshop, make sure you pick the registered ones, and you will see they are perfectly aligned (including rotation). Have fun.
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