The thing about live rock is that it's already got anaerobic bacteria, deep inside it. This is why it's an effective filter. Rubble would have less, naturally, because it's smaller. I would use the rubble in the refugium, under the algae, for the critters to live and breed in.
You are going to have a sump also, correct?
I would use the canister to run media, like carbon and/or phosban, and maintain it monthly.
With 100+ pounds of live rock and that skimmer you have, you are well on the way to having a strong system.