Mod Manager is great for getting the ZIP files into the proper game folder. It also gives you a preview of what the Mod will look like in the game.
CMMOS is a quick way of running the batch file to swap the texture.
They both have their ups and downs. In my opinion, Mod Manager is easier to use if you are a Mod maker. However, it's more difficult to keep organized. If you like to have everything where you can see it, scrolling through a hundred Mods looking for the ones you want can be tedious.
CMMOS does a better job of managing things. If you are a Mod maker, you must understand its system of rules and go through a clearance process before releasing your creation. It also requires a complete set of BMPs be present in the CMBO BMP folder for each Mod. This eats up a lot of space on your hard drive.
So, if you have the room on your drive, put the ZIP files into the Mod folder for Mod Manager and use it to install the BMP files. Use CMMOS to quickly change textures. If you have a limited amount of hard drive space, stick with Mod Manager.