I use a Mac, and spend equal times on the Mac side as my Win 7 Boot camp side. I figured out this trick. Set up your initial collections/books on one computer and sync it. Now go to the second computer and make sure it is empty (no books or collections), then hook up your Reader. Drag collections from your Reader into the Library software (from the list/tree on the left hand side): you have imported your collections into the new computer. Now, go the the Sync item and pick the collections you want to sync (should work for the whole library as well). Viola! Now each computer will see the same collections and sync appropriately. It should work for the whole library as well, but I keep everything in collections to keep it tidy. If you add a new collection on one computer, you can just drag it to the new one before you sync up.
I hope this is clear enough: maybe I can make a small screencast if it's a bit confusing.
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