MO is a very powerful tool. I have no .esm files in my Skyrim data folder, the originals are backed up on another part of my hd. Yet Skyrim runs just fine because MO is using my TES5edit cleaned .esms in it's mod structure to run the game. It's a little tricky to figure out the way MO works at first but once you figure it out I think you might like it. The tricky thing for me as a first time user to figure out was that SKSE was both a separate program and a MO "mod". Parts of SKSE still had to go to the Skyrim folder but the rest went into a MO mod, including the all important skse.ini to make the memory patch work.
Setting up a "default" profile and then cloning it for use with other profiles is also a nice feature. I set my default to have my cleaned Bethesda .esms, SKSE, SkyUI, iHud, and Unofficial Patches. Then I cloned it, and started installing mods. Now when I start a new profile I clone the default and then just start checking off mods I want to use since they're already installed in the mods folder. It can separate save games for each profile so there's no looking through a list to figure out which character is which. LOOT can sort your order from MO. TES5Edit, Wrye Bash, etc works through it as well. Testing a mod is as easy as cloning the default profile, installing the mod in the new profile, LOOT it, clean it if needed, Bash it if needed, run it. Don't like it? Uninstall the mod, get rid of the profile. Like it? Switch profiles and check the box, LOOT the order, etc. Gopher has some nice videos about how this works in his Mod Organizer playlist.
Try it out, get frustrated with it like I did, then after using it for a little while it'll "click" and you'll never look back.