A merged patch is easy with FNVEdit.
From http://steamcommunity.com/sharedfiles/filedetails/?id=158611358 (For Fallout 3 Editor but the instructions are the same)
Ok, in order to create a merged patch you're going to need this program called FNVEdit.
Once you have that program, extract the contents of the archive into a folder. Once complete, run the Fallout 3 Edit program, as an administrator if required. Now once the program has opened up, a window should appear. In this window should display ALL mods that you have in your directory, enabled or disabled, it doesn't matter, it will be in that list. Just ignore it and click 'OK.'. Now it should begin loading your mods into Fallout 3 Edit application. Now the time it takes for all mods to be loaded will vary on the amount of mods you have installed and the size of those mods. Once the program has finished loading all of your mods; In the left-hand side of the screen should have all of your loaded mods on there, simply right-click, at the bottom where it says 'Other' click there, then click 'Create merged patch'. Once clicked, you should be prompted with a notification asking for a name for the merged patch, simply type a name for the merged patch, I recommend just calling it "Merged Patch". Click OK. Now exit out of the program and click OK to save changes.
We're not done yet, there is one final step: Open up your desired mod manager (FOMM or NMM) and go to the bottom of your load-order, at the bottom there should be your merged patch with the name you gave it. Simply activate/check this merged patch.
*WARNING: Maintain merged patch at the bottom of your load-order at ALL times! Failing to do so will inevitably result in a crash-upon-start up 100% of the time! ALWAYS keep your merged patch at the bottom of your load order!*
