I don't think there is any "best" way or everyone would have their tanks set up like that. Ultimately, based on your own research, you are going to have to decide what you want to do and why you want to do it.
There have been examples of what different people use in their sump/fuge/canister filters.
Personally I find canister filters to be useless for anything other than running carbon - my opinion. I have 2 large tanks set up. On my 230g I have miracle mud, various macro algeas, and live rock. I also have a 4-5" sand bed in this tank. I have mostly LPS, softies, anemones and of course fish in this system. On my 190g I have just live rock and live rock rubble with some chaeto algea in there. This is a high flow tank that I run bare bottom with some mushrooms, LPS, anemones, fish and a few sad SPS that I haven't lost yet due to some heat and skimmer issues this summer.
On a 100g tank that I am just setting up I am just going to use my sump to house equipment and for extra volume. Period.
So you see it depends on what you are trying to accomplish, and why. At the end of the day it is your choice and your decision.
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