It would appear there are two kinds, new or hacked objects to download, and gameplay hacks/changes. I don't have the Sims myself, so a lot of this guesswork. I've seen mentions to a download folder, that I think is where your supposed to put new mods, not just in the root directory. It's also possible that some of the mods are alterations of data files the game already uses, and in that case, you'll probably have to replace the file in one of it's data folders. If you do that, keep a backup of the file you replaced around, in case you ever want to undo it. Sometimes new mods can make a game unstable.
I'd suggest trying the root directory first, which is where I'm guessing you've already tried, then the downloads directory (if there isn't one maybe create one for it) and then try searching to see if there is already a duplicate file with that name. You could do that by hand, but the search option in windows is usually faster if you don't already know where it is.
I also found this on the site, so try this first:
http://www.modthesims2.com/showthread.php?t=62053
Does anyone know how to do this properly? 
