DO NOT MERGE WITH TESVSNIP!!! Read this forum. People have lost hundreds of hours of work after using TESVSnip.
So my question is how to merge two esp files in one. For example if you have MyMod1.esp and MyMod2.esp how can I merge them so it will be MyMod3.esp and MyMod3.esp will consist MyMod1.esp and MyMod2.esp. Help !
There isn't an easy way right now. A tool (TESVGecko) is being worked on that will help. Now, for small merges what you can do is make a backup of MyMod2.esp and stash it somewhere, then load MyMod2.esp as the active mod in the Creation Kit with MyMod1.esp also checked. Then, you need to rename each object that is created by MyMod1.esp so that a new form is created. Then when you save, those new forms will be saved as part of MyMod2.esp, since it is the active mod. When you're done, MyMod2.esp will contain all the forms it started with, plus all the forms that were in MyMod1.esp that you have copied into it via renaming. Then if you want you can rename MyMod2.esp as MyMod3.esp.
You can also setup and use http://www.creationkit.com/Version_control (see also http://www.sureai.de/development/tutorials/skyrim-creation-kit-version-control/?lang=en), which can help with merging although it is more geared toward larger projects with .esm files.