It seems with the newer version of the Arduino IDE you can now download a library and add it without having to unzip it (Add .ZIP Library...). It also adds the library to the proper place in the Arduino User directory.
Further, it seems to not care about hyphenated folder names. I download the latest version of NT7S's Si5351 library into my downloads directory and by adding the library as above and it worked just fine. User libraries are now listed in a section called "Contributed libraries" which shows up when you click "Include Library" on the above menu. This should make things a little less confusing.