Yeah--unfortunately, as of now only Kontakt Player instruments can be loaded using the "Add Library" option in the library tab. So right now you have to manually load the patches, by clicking on the "Files" button, then "Load...", or using Kontakt's browser tab.
If it's of any help, Kontakt also has a quickload feature, which allows you to drag your favorite libraries into a list (which can be organized into folders). That's what I use, even with Kontakt Player libraries, because of the organizational capabilities. Of course, you don't get the pretty library tab art... ;)
In terms of installation, I kept the engine RAR and the samples RAR files separate, so that if there are updates in the future you don't have to redownload the whole thing. As long as you have all the RAR files in the same place, and then extract the "EEB-Engine.rar" file and the "EEB-Samples.part1.rar" using the "extract here" option, everything should install properly.
The reason you only need to extract the part1.rar of the samples is because it's a multi-part RAR file--when extracting the first part, it automatically extracts the rest of the parts, too.
Let me know if you're able to get it working, or if you need more detailed installation instructions. The user's guide PDF
(click here to download) has a section with installation instructions, too.