Manual ordering - not using LOOT
Make sure sort by priority is on look in the Left pane, the little lightning bolt with + or - - has something overwritten + overwrites everything above it
If you select one of these mods and scroll through your modlist you will see other mods in highlight in green, they are being overwritten in some way by this mod. Any highlighted in red are overwriting the mod you selected.(Group/Drag these one together in the order of overwrite you prefer.)
Group all your mods
Unofficial Fallout 4 Patch Armor and Weapons Keyword Community Resource {Settler mods} Settlement Keywords Expanded
then all your Textures or Meshes
then all your Weather mods
then Player mods - like cbbe, body textures clothing
then ui and gameplay
when you see a -lightning double click go to conflicts tab, if the mod you have selected is being overwritten by what you want then all good otherwise drag it below the offending mod. Try to keep all the mods that overwrite each other together. It will keep you sane.
i.e. Caliente's Beautiful Bodies Enhancer -CBBE- Caliente's Beautiful Bodies Enhancer -outfits- Additional Body Textures - Ghouls and Old people Vault Booty 1.0.4eaw Experimental Atomic Wedgie
so in that example the Vault Booty overwrites the CBBE vault Suit Ghouls and Old people look like they are supposed to and CBBE gets it updated clothing pack.
To keep things ordered (visually) I create empty mods (that are not enabled) and I name them appropriately, then move the mods under them.
In the left pane click create backup then click the sort box everything should now sort and locked mods migrated to the top this delets the plugins.txt i.e. Keywords, homemaker, robot defense, snap and build basically things in italics move them to the top then Unofficial Fallout 4 Patch then your other esp files
Only thing else you can check for is in the data tab, things in highlighted red. They they are esp's being overwritten by some mod. If you hover the mouse over them it will tell you which mod is doing it and you can verify in the left pane if that is the correct overwrite, If not you have to move the mods in the Left pane to change the overwrite order.
