SyncTwoFolders is easy to use, even if some of the commands are a bit advanced (you don't have to use them to use the application). All you have to do is select which two folders you want to sync together by pressing Choose Folder for a Source and a Target. Then you can choose to delete certain files that began with certain characters, ignore items, replace files with one more recent and so on. Once you have decided what you want to do, just hit the Synchronize button in the lower right hand corner and they will merge files, while staying separate folders.
The window design is a bit sparse, but that doesn't really mean much. It does what it claims to do and that is good enough for me!