I don't think there is an easy way to "merge" them. But you can do it manually. Do a save to disk from one machine of all the books that aren't on the other. Then use the Add books, one per folder, and point to that save to disk area... it will pull in all the books and metadata.
You can have two libraries if you want. Or, you can have two copies of the same book in the library that is not a problem. But, seriously, just remove the DRM from the amazon books and keep the books you own. (Yes, this is illegal in 34 countries.)