Can you use a coarse foam pad and then the 100 micron pad followed by the 50 micron pad as the first filter in a canister filter?

Yes, you can use a coarse foam pad and then the 100 micron polishing pad. If your aquarium water is clear of free floating particles you may not need the 50 micron filter pad. If you do want or need the 50 micron filter pad the order you said is correct