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I have the Mac Apps version of Crusader Kings, and I would like to know how to download mods. I don't know where to put the mod, since there isn't a Mods folder.

CK1 doesn't have a mod-folder, you need to overwrite your existing files in order to play a mod. It is therefor recommanded that you make more then 1 installation of the game if you want to add a mod.

Since I don't have a Mac, I don't know if the mods work for the Mac.

Mod can be downloaded by clicking on their downloadlinks. Many mods are no longer active and may have broken downloadlinks, that is because this is a very old game.
 
How would I go about overwriting the file?

You simply extract the mod files with winrar or 7zip in your CK1 folder. I have no idea about unzipping files in a mac environment, it might differ from Windows.

Make a copy of your original version first.