Andrew had a great summary as well and completed a few facts about how I am also running (like I said, I pretty much followed his lead). Except, my tank is pretty new also (~6 months running).
All filtration I have running in my system (nothing off line): Skimmer (wet), carbon, Seachem Purigen (thought it couldn't hurt to run in my tank), about 35# / 6" DSB in fuge, Algae scrubber. Also, I had a lot of bio media spread out in my tanks (ceramic fluval rings mostly) - I threw all active biomedia into my sump when my ammonia spiked.
So moral of the story is, I would not pull anything offline except macroalgae. THAT assumes you are doing a display tank hypo treatment (in - fish, rock, sand...out-all inverts), which is what Andrew and I are doing.
If you're pulling rock/sand out of tank, hm. I would probably put as much active biomedia as you can in your tank, pull fuge offline, and just do an old fashion hypo treatment (no inverts, rock, sand). Proven and way easier to control. You will just need to make sure there is a full fallow period with rock/sand/inverts, however, as you will not be treating the Ich that survives here and must allow them to cycle through without hosts and die completely (I believe you raise temperature for fallow tank treatment).