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The only two real buttons you will need to use is "Sort Plugins" and "View Last report".
Sort Plugins- Basically sorts your lord order which is in the data file section within the launcher. Let the process run till it's finish. Once then LOOT will generate a report on things right or wrong with the load order. If you see anything wrong within your load order like dirty edits for example. I highly recommend watching Gopher's videos on LOOT
View Last Report- Basically LOOT saves it's last generated report after you run LOOT through the Sort Plugins option.
I think you are mistaking Mod Organizer and SKSE. You don't need to run LOOT to latter. It is just an script extender. It does not have any UI to run SKSE and does not even detect it presence.
Ignore the comment about "sort plugins" option. That is related to MO and not even recommended, because MO sorting tool is usually out of date from main LOOT release.
Otherwise instructions are good. Just run LOOT, when it is properly pointed to your Skyrim installation.
Yeah. I tested the beta release and it messed up my load order royally. Luckily I had stored the correct order with MO, so it took only a second to fix.
Do32Sierra.
You can run LOOT from NMM but you should run LOOT separate. NMM cant detect the change in load list if you dont reload NMM.
You can also add one powerful and usefull tool called Wrye Bash.
Also running latest MO V1.3.3, not the version in nexus and about to upgrade to V 1.3.5.
Also have LOOT Version 7 installed (not MO sort) as well.
Only once did it sort the plugin order wrong, at start of using it, now it is back to the normal load order.
Check this video from Gopher.
Little old but it will help you.
https://www.youtube.com/watch?v=SzoyWugzZAw