It is always a good idea to use a mod manager. It enables you to uninstall mods without damaging the main structure of dcs. I always have my folder as Mods, then check the jsgme ini file for the correct path etc.
When you download a mod, you should check the structure that it is in, just in case there was a mistake in packing ie too many folders.
For your cockpits, you need a Liveries folder in saved games. Then you can add the cockpit there. Look at some of the posts concerning installing mods to give you an idea of the folder structure in saved games.
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Cheers