So I've recently finished another mod that I have been working on, and I had a thought that it would actually go better with another mod I've already created and released, and that I could save some people (myself included) some time and effort and free up an .ESP slot by merging the two mods together. However, I was wondering if this was possible at all?

Basically what I want is "add" Mod 2 into Mod 1, so that Mod 1 has both the effects of Mod 2 and Mod 1 with only 1 .ESP/BSA file. I thought I could do it if I used the CK, load Mod 2 and Mod 1, set Mod 1 as the Active File and then just save it - but will this work, and allow me to update the Steam Workshop version of Mod 1 without having to make a new upload?

I don't know about the whole steam workshop uploading thing, I had to upload my mod 5 times to steam because it wouldn't let me update it. But the only legit way I know for merging is Version Control but that is based towards bigger mod merging and is kind of difficult to get working. What exactly are these mods? Like dungeons, quests, player home, etc.

One is a set of Custom NPC followers, and the other is a mod which adds a couple of perks and modifies the Vanilla followers to be less useless (especially in comparison to the followers from the other mod), like making the sneaking/stealth companions not affect stealth etc.

The Custom Followers is an .ESP+BSA, and the other is just an .ESP.

Close, but it's a little more involved: see the wiki page on http://www.creationkit.com/Mod_Merging.

Well I suggest trying to manually merge it like the page says(just copy-paste everything over). If you don't want to and you think it's too much to do manually then you can try to get version control working but be warned it's not an easy task.

Ch0k3h0ld posted some good information on rolling two esp together, but it was more cell + cell mods, not actor mods.
I can re-post it if he doesn't show up in this thread.

STEP ONE - MAKE BACKUPS OF YOUR ESP FILES.

The techniques of merging two esp files into each other is very dependent on the types of edits and objects contained in the mods. NPCs are actually relatively complex to copy once they are completely set up as actors since you have to find and copy all of the parts. It simplyfies it a lot if you create a name for each custom form and object in the Object Window that is easy to locate again later. I generally start each ID with 001 and and an indentifier for the mod or cell. So if I have a blacksmith in the Dovahkiin's Warehouse the ID might be something like 001WarehouseBlacksmithMonica. Since she works 24/7 right now, her AI package is 001WarehouseMonicaServices24x7. And so on through relationships, factions, work area markers, merchant chests, outfits and so on. I can get all of those together at the top of the Object Window by entering 001 in the filter and selecting All at the bottom of the tree.

Once you have all of your custom objects named so you can find them, open your two files together in the CK with the larger more complex one as the active file. You need to pick which one is easier to copy from based on what you have done in them. I'm going to assume you don't have any cells to copy. The information Shalani is referring to was mostly focused on interior and exterior cells, which take a different approach. I also suggest you do not try to copy entire vanilla cells but instead re-create what you have done in those by renaming or moving the items directly in the cells. Say if you moved a tree in the original, just nudge it a little and it becomes part of the merge esp. You can see the objects that you modified because they will all have asterisks next to their IDs. But I digress. If you have custom cells, that is another conversation. It doesn't sound like you do.

Once you see the objects you want in the Object Window, you need to rename them not duplicate them or the links will be broken. I generally change all of the 001s to 002s or something easy like that. Once you rename them, they belong to the active esp. Leave them with unique IDs so they don't conflict with the mod you are copying from. Otherwise if you try to open them up together again they will have conflicts. I usually discover something I missed in the first pass. This process will not modify the names in the non-active esp as only the active esp is modified. As long as you use an esp to copy from it does not create a master dependancy. If you do somehow create a master dependency - probably by using an esm to copy from, it can be removed in the CK. Go to the data window and select the esp. The master dependancies are listed over to the right of the plugins. Select the one you want to delete and hit ctrl-del. Then load the esp as active and save it.

I hope this is all helpful. Remember that you made backups in Step One and don't panic if the result crashes the game on the first try. Just go back and try it again. Merging plugins in the CK can be a lot of work and sometimes yields unexpected results. We really need some new tools since TESVSnip is officially persona non grata.

The mod I'm merging the other mod into is the more complex one- its my Paragon's Follower Pack (PFP) from the Workshop - it contains Custom NPCs and a few custom items, so that isn't the the one I'm moving.

The one want to put into the PFP is simpler tweak of the vanilla followers - all I did was give them a few perks (gave them their racial etc.), modified some of their spell lists, and fixed some things to make them less useless and make more sense (IE: I marked the Sneak Companions as "Doesn't Affect Stealth" and fixed Lydia being marked for opposite gender animations).