Enterprise Data Synchronization with Microsoft SQL Server 2008 and SQL Server Compact 3.5 Mobile Merge Replication by Rob Tiffany would have to be the ultimate guide when it comes to setting up and tuning merge replication between SQL Server and SQL Compact. Starting with the basics of what and how merge replication works, Rob then drops into a great level of detail that will be sure to help you if you get stuck. I would definitely have this book by my side when working with merge replication.