This video shows you how to install and use my Mod Merging script for TES5Edit.
Download link: https://www.nexusmods.com/skyrim/mods...
TES5Edit link: http://www.nexusmods.com/skyrim/mods/...
User Reports & Testing link: http://forums.nexusmods.com/index.php...
This script is still fairly beta, but should work for the majority of merging tasks. I'd highly recommend you refer to this thread on Nexus Mods for questions/problems:
http://forums.nexusmods.com/index.php...
___[What it cannot do]___
This script cannot deal with corrupted data (merging a mod with corrupted data will cause CTDs when Skyrim starts)
Merging mods with scripts in them often won't work. It usually does, but it sometimes doesn't. I'd recommend against merging heavily scripted plugins.
If you want to merge multiple mods that modify the same leveled lists you need to use "Create Merged Patch" in TES5Edit and merge them into that patch.