You figured it out pretty well.
Yes, you mask off the areas surrounding the indentations, then you mix up the
thickened epoxy filler and use another layer of tape to "shape" and hold the epoxy
fair with the surrounding area while the epoxy cures.
When you epoxy has hardened, peel off the two layers of tape and your indentation will be nearly level/faired with the surroundings.
The shaping/holding tape is not so important on nearly flat deck areas, but on rails
noses and other "non-flat" areas it works very well.
A little work with a file on the epoxy repair material, a little sanding, a couple of coats of matching paint and you have a professional looking repair.
Hope this helps,