you need to use the jsgme utility to install and uninstall mods so it doesn't mess up your game.
find it here:
http://www.subsim.com/radioroom/showthread.php?t=156898
next when moving mods into jsgme you need to double check the file path for the mods by opening the folder and you should see a file there called "data", if the data folder isn't there then the folder you see is most likely going to be the actual mod folder that needs to be put in jsgme.
it should look like "mod name/ data" and not "mod name/ mod folder/ data"
some modders use double folders and some don't so you need to check this. also some mods have different versions to pick from and some have extra add-ons included so never just unzip a mod straight into jsgme, unzip it to your documents or desktop to open it and confirm you are adding the correct folder to jsgme.
welcome to subsim
good luck and happy hunting