Simply download and install a mod, itself a painless operation with Nexus integration, then rearrange the order of each mod in the left hand pane until any potential conflicts are removed. MO uses a 'virtual file system' that generates your modded game each time you load it. Mod Organizer is the best utility to happen to game modding since the pencil and paper was invented! No more will you have to struggle with overwriting files as you incorrectly install mods.
It has steadilly improved with each release and is now widely accepted as the best Mod Manager for Skyrim. The profile system for virtual installs is a must have. It is specifically designed for people who like to experiment with mods and thus need an easy and reliable way to install and uninstall them. Mod Organizer MO is a tool for managing mod collections of arbitrary size.