Jedi-
Just run both procedures on each mod - as long as you don't clean what is on the don't clean list then you are good. You don't have to save the mod after cleaning and that will undo the cleaning. You could even highlight what it gives you and show the mod maker what it found. I've done that but to lukewarm reception at times.
If not on the do not clean list then both procedures should be harmless.
KC33-
Just read the tutorial linked above then come back and ask if you have any questions. Again if not on the do not clean list then I clean regardless or check if needed at the very least, but if needed it gets cleaned.
The do not clean list:
# Do NOT clean any FCOM files that come in the FCOM archive. (or other overhauls)# Do NOT clean SM Plugin Refurbish…unless you really understood this guide.# Do NOT the unofficial patches (UOP, USIP, UMP). They have already been cleaned.
I see also on the tutorial not to clean these as well:
ArmamentariumArtifacts.espMart's Monster Mod - City Defences.esp (author says to not clean)Mart's Monster Mod - Gems & Gem Dust.esp (author says to not clean)Mart's Monster Mod - Hunting & Crafting.esp (author says to not clean)BG2408's mods (LAME, RBP, Integration)Oscuro's_Oblivion_Overhaul.esmOscuro's_Oblivion_Overhaul.espFCOM (None of the .esp/.esm files should be cleaned)
And above was posted advice not to clean book jackets, but not why.