Using Quartz Composer Plugins
Quartz Composer plugins (which end with .qtz) should be installed in either your ~/Library/Compositions/ folder.
If you bought Acorn directly from Flying Meat, there's a super easy way to do this. Just drag and drop the .qtz file onto Acorn, and it'll ask if you want it to be installed or not.
If you bought Acorn from the Mac App Store, it's sandboxed and you've got to do some extra work. Go to the Finder, choose the Go menu, and then press the option key. A new menu named "Library" will show up. If you don't already have a Compositions folder, you can create one and put your .qtz file in there.
You'll need to restart Acorn to get your new plugins to show up, and when you do they will appear under the Filter ▸ Quartz Compositions menu item.