Mod Merging
There is currently no tool available for easily merging Skyrim mods. No tool that works as quickly, easily, and effectively as TES4Gecko does for Oblivion. Hopefully a programmer write a utility for merging Skyrim mods at some point.
Options:
(1) Manually merge in the CK.
Open up the two or more mods in the CK at the same time, with the file you want to merge the data to being the active file. Select an item you want to copy and give it a new name. When asked if you want to create a new object, say yes. Be sure to copy every little detail that you want to merge. Let's say you want to merge your NPC into another mod. You may not be able to just copy the actor object into the other mod and get away with it. Your actor might arrive naked, confused, broken, and helpless. If your actor has custom armor, custom AI packages, custom dialog in a custom quest, carries a custom sword, and belongs to a custom faction, you better copy all of those objects into your mod too.
This merging approach is rather time-consuming.
(2) Merge mods with TESVSnip.
This utility is easy to install, and fairly easy to use once you figure out how the interface works. This process is not fully automated. After loading up two or more mods in the window and expanding all the branches, you still have to select branches or individual edits to copy to the other mod. You have to be careful about creating duplicate FormIDs within the merged mod. You can edit the FormIDs so that they are no longer duplicates. There is a spell that you can use to locate duplicate FormIDs before saving. You can save your mod with a new name, or save it on top of one of the mods you are merging to preserve its name and protect dialog that may be attached to it.
Merging mods this way can still be slow and problem-prone, but it is faster than using the CK. TESVSnip was used for some pretty heavy-duty modding in the days before the CK was released. It can do many of the things that TES4Edit could do for Oblivion.
Here is the link to an illustrated tutorial that explains some of the details on how to merge mods with TESVSnip: Mod Merging with TESVSnip.
If you are working on a modding project with multiple modders and your mod is very complex and does not merge easily using the existing methods, you may consider taking turns working on the file. One modder at a time would work on it while the others would refrain from working on it since anything they built would be very hard to merge in. Alternately, you may figure out what types of work you are doing that are easy to merge. One modder at a time would work on the main file with all of its difficult-to-merge content, and the other modders would build pieces of the mod that you had proven were easy to merge to the main file.