Okay, starting from a default 7dtd install, you go to the root 7dtd folder at c:\program files\steam\steamapps\common\7 days to die.
From there you open data, then prefabs. This is where you stick everything from the compopack archive folder called "PLEASE copy all files from this folder into your 7d-prefabsfolder" (over 2000 files).
Now go to wherever you put the NitroGen program. I stuck it on the desktop for convenience. Open that folder and then the resources folder. This is where you stick everything from the CompoPack archive folder called "Nitrogen-files" (only 3 files).
Make sure both times you are only putting the contents of the folders, not dragging the whole folder over.
To be able to make large maps (over 4k) go to the NitroGen folder and make a backup of the start.bat (or whatever it's called) file, then edit start.bat so that it says:
java -Xmx12G -jar nitrogen.jar
Where the 12G is, put whatever you want as long as it is at least 4GB less than your physical RAM. So if you have 8G, put 4G. If you have 16G like me, put 12G. If you have more than 16GB, you can make it higher, but I've never seen NitroGen use more than 10GB on even the largest, most complex maps. And don't forget that you need 64-bit Java installed (not JavaScript).
When you want to make a map, use the edited start.bat file to start NitroGen.
In NitroGen, use the Open Output Folder and Open 7Days GeneratedWorlds Folder buttons, and in the second case you will have to dig 1 level deeper by opening the actual GeneratedWorlds folder. Then you can just copy your new world from Output Folder to Generated Worlds. If this sounds a little silly, it's not my fault.
Make sure you set the prefab list (top right under Advanced) to the appropriate selection with the drop-down (the latest is a19.1 cp 46, as far as I know at this moment), and set scenario (lower down) to none.
Try a few maps, check the previews, start a game in each. If you still have problems, come on back.
Edit: If you're having problems with the DL links at the beginning of this thread, poke me and I will see if I can help.