If you use the mod picker program that comes with the SE4 CD, you can pick and choose the mods you want to use.
You put each mod in it's own subdirectory. If the mod changes a file, the subdirectory will contain a new file. If the mod subdirectory doesn't contain a certain file, SE4 uses the file from the default directory.
Once you've got it setup like that, you can see two mods side by side. If they don't modify the same file, it's easy to put them together. Just copy files over.
If they do modify the same file. Now you have some work to do. The data files are all text. You can cut and paste, but you have to be careful. Better make a new directory just with your merged mod.
I have to admit I tried to merge Suicide Junkie's Pirates and Nomads with the Space Monsters. But I didn't have much luck
