This video shows you how to install and use my Mod Merging script for TES5Edit.

Download link: https://www.nexusmods.com/skyrim/mods/37981
TES5Edit link: http://www.nexusmods.com/skyrim/mods/25859/
User Reports & Testing link: http://forums.nexusmods.com/index.php?showtopic=1033740

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?/topic/904953-how-to-merge-multiple-mods-with-multiple-master-files

____[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.