My advice is to learn the data structure of Skyrim so you can undertsand exactly what the program is doing. Once you have done that if you have any questions or doubts you can you can right click a mod folder or folders within Mod Organizer and go to "Open in Explorer". Then you open your mod archive in a seperate window and double check to make sure it installed correctly. You should know how to do this anyway in case a mod doesn't come with an installer and you need to add or remove any files. Also, MO doesn't care if your mod is in one folder or a hundred folders. Every file gets added into the emulated data structure. So those files are essentially being merged anyway. A merge physically merges the files and the other copies are destroyed. This just means you can't modify the file priority within that single mod without reinstalling the mod. It also means install order is important. However unless you understood how MO's file structure system worked than install order was probably important for you anyway. Bottom line I recommend learning what you are doing. Learn the Skyrim file structure and learn the MO file structure. Some tips: 1. Look at the Priority in MO to see which folder in MO has priorty. Look at the flags to see what files are being overwritten. 2. To gain more control over file priority go to Archives and check all the .bsa. This lets all the files in that bsa follow the priorty order designated in MO. That's normally a good thing. Note that this makes priorty even more important to manage in case a mod auther assumed he could rely on his loose files having priorty. You have to look and make sure the files you want are overwritting other files. I usually set my file priorty to the same as my load order and then adjust things based on what I see. I usually let mods I care about more take priorty or if I know some particular information about compatibility between mods I take that information into account. It's like messing with your load order but more detailed. I love MO by the way. Such a great program.