I have messin around with my folders and stuff...where should the Mods folder go?  And what exactly is it?  Is it like a "safe spot" to turn off my mods and play the regular game?

you have to make a Mods folder in your Game Data folder.

FoC or original?

im pretty sure it works for both.

i dont have FOC but i think i read somewhere thats what you have to do, just like the original.

You can create either a mods folder (as directed for the latest patch of stock EaW) and use a specialised shortcut to run the mod, or you can create an XML folder in your DATA folder instead, and this DOES work for both as well.