Do I have to do anything special to make the U3 and non-U3 versions work together?

No. Gaviri SearchOS for U3 and non-U3 is plug and play. Simply connect the drive and start PocketSearch. If you are using the U3 version, Gaviri SearchOS will start automatically and when you connect another U3 or non-U3 drive, Gaviri SearchOS will see the index of the newly connected drive, import it and tell you that the index has been added. When you search you will be simultaneously searching the indexes of all connected drives – U3 and non-U3.