Joel,

For merging to work properly, meaning that you have identical photos in two libraries and merge them together, and expect for example metadata change from one to combine with Adjustments from the other, then the first thing to know is that they have to original from the same library. You can’t import the same RAW files into two separate libraries, then merge them and expect the files to match up.

The workflow would be to import images into one Library (let’s call it your Primary Library), then drag/export a project/album/whatever out of that Library to the desktop, which will create a self-contained library (let’s call that one Exported Library). You can open Exported Library on one machine, and make changes to some or all photos, and simultaneously open the Primary Library on another machine, and again edit some or all photos. When you then later import the Exported into the Primary, and direct it to Merge, it will look for conflicts. If it finds conflicts, it will ask which Library gets priority. If you aren’t sure, you should cancel, and Add instead of Merge, and manually compare.

Check out this post I wrote when Aperture 3 first came out, Aperture 3—A Game Changer (Multiple Macs, Syncing Projects, & More) for a little more info on this, and also the forum thread Syncing “Portable” Library + Master Library: Strategies?.

If that doesn’t answer your question, I think the next detailed tip I’ll write may be on this topic.