Awesome. Here's what I would do.
First things first, we need to add the one library to the other. The easiest way is to go into iTunes, and import the 2nd library. Unfortunately, this leaves us with duplicates of many songs. So, we need to add just the songs that aren't already in the library.
In windows, you can just drag the contents of one folder into the other, and it will add the files. OS X differs, in that it will overwrite the entire folder.
So what you want to do is pull the main library into Windows, and while you're in Windows, add drag the contents of the iTunes folder into the iTunes folder of the main library. It will ask you if you want to overwrite files. choose "Ignore all" or "No to All" to make it go faster and to keep your old library info. That puts all of your music into one place, without duplicates.
Then, just pull the folder back into OS X, and open up iTunes. All of your music files will be there, but only what was in the main library will appear in iTunes. From there, just go to file > import and import your whole iTunes library. iTunes automatically skips files that are already in its database, so it will only add the new ones.
Hopefully, this made sense and it helps. Just met me know if you get confused or anything.