I'm wondering about this too. I am new to MO and STEP in general. I am following the SR:LE guide as well.
a. After moving the cleaned esm's (from Skyrim\Data) to ...\Mod Organizer\mods\Cleaned Vanilla ESMs
b. Restoring the dirty esm's to Skyrim\Data and renaming them to their original name
I see a Warning Triangle on the Archives tab in MO. (I have Dawnguard.esm, Hearthfires.esm, Dragonborn.esm, checked on the plugin tab .. but not the Highres..esp's)
In the left side I have the mods:
Cleaned Vanilla ESMs
Skyrim Script Extender 107
Vanilla Optimized
Dawnguard Optimized
Hearthfires Optimized
Dragonborn Optimized
HRDLC1 Optimized
HRDLC2 Optimized
HRDLC3 Optimized
Seshons Mem block logger (added this on my own to track mem block usage)
Do I leave the ESMs checked on the Plugins tab and ignore the archives "warning" triangle?
Edit: I tried finding the Skyrim Revisited instructions but don't know my way around the STEP forums very well. In any case, I just unchecked the ESM's in the plugin tab (assuming the Optimized mods will replace them as long as they are activated in MO)