TES5Edit Cleaning confusion

[alocrius]

This is something I'm confused about. Paricularly this part of the Neovalens guide for cleaning the main esm's:

 

Start Mod Organizer.
Select "TES5Edit" from the drop down above the right pane and click [Run].
Right-click inside the file listing and select "None".
Check the box adjacent to Update.esm and click [OK]. Wait for the message "Background Loader: finished" to appear in the right pane.
Right-click Update.esm and select "Apply Filter For Cleaning". Wait for the message "[Filtering Done]" to appear in the right pane.
Right-click Update.esm and select "Remove Identical To Master Records". Wait for the message "[Removing Identical to Master records done]".
Right-click Update.esm and select "Undelete and Disable References". Wait for the message "[undeleting and Disabling References done]".
Click the [X] on the title bar to close TES5Edit.
Verify the box adjacent to Update.esm is checked and also that "Backup Plugins" is checked then click [OK].

Update.esm has now been cleaned, meaning that any improperly removed records or edited records that were identical to the base Skyrim.esm file have been fixed.
Repeat the process above for all of the DLC ESMs in order selecting only one at a time. Do NOT attempt to clean Skyrim.esm itself.

 

what does this mean.  Do the cleaned vanilla esm's get checked in plugins of actual mod organizer plug-in window?  Seems they dont if I want skse to launch, so what exactly are these files doing and how do you activate them and what EXACTLY are these files supposed to be named as you create them because the guide doesn't specify and it's a bit confusing..?  I know this is a weird question just thought someone here might be able to enlighten me.  Thanks for any help.

Edited July 27, 2014 by alocrius

[DoubleYou]

What does that have to do with DDSopt?

 

At anyrate, if you don't understand Neovalen's instructions, you can follow the instructions for cleaning them in the STEP Guide here, here, here, and here.

[alocrius]

Yeah, sorry, wrong section. Thanks for the links.

[alocrius]

What does that have to do with DDSopt?

 

At anyrate, if you don't understand Neovalen's instructions, you can follow the instructions for cleaning them in the STEP Guide here, here, here, and here.

Per your instructions, would those cleaned esm's get a check inside the plugins window?  Because they have the same name as the originals so is that one check in the plugins accounting for the original and the cleaned.. do you see where my confusion is?  I guess i dont understand what the plugins window is doing.

Edited July 27, 2014 by alocrius

[DoubleYou]

As long as the cleaned ESM mods are checked in the Left Pane and the Plugins tab, it'll be fine.