Always run
LOOT after you have installed all your mods (or after installing a new mod mid-save to position it correctly in the load order). LOOT is the new beta version of BOSS, and it works like a charm, without the need of BUM or anything else. Run it and everything is sorted!
If you install more than one mod that alters levelled lists (what "respawnable" NPC's carry, like bandits), then you must (re)build "Bashed Patch, 0.esp" with
Wrye Bash.
Remember to install
SKSE, as most mods will require it - you will always have to run the game with "skseloader.exe" for it to work. You should also add this:
[General]
ClearInvalidRegistrations=1to SKSE.ini in C:\Program Files(x86)\Steam\SteamApps\common\Skyrim\Data\SKSE (if you don't have it, create a new .txt and rename it to SKSE.ini) so it can help avoid corrupted saved games if you uninstall scripted mods.
If you plan on using HQ texture mods, you should use
Optimizer Textures once you have installed everything - I use "maximum profile" and resize if bigger than 2048.
If you have to uninstall scripted mods throughout a game, use
Savegame script scalpel to clean the saved game of orphan scripts. Load the saved game, let it analyze until it says "analysis complete", then click on "Remove unattached instances", until it says "removed x number of instances" (bottom-right), then click on "Remove instances", tick "Remove instances with undefined classes only", then remove. Close the program, then go to your saves folder (my documents), move those last saves you edited (not the ones that start with EDIT) to your desktop (for example) then copy their name (without file extension) and paste it in the new EDIT files in saves folder (renaming them like the originals).