Just copy the Games drawers containing the iffs to the new location using Dopus. They all have the same directory names, so over-write the destination drawers and the iffs will be dropped into the game directories without changing the destination's contents.
This thread may be of interest:
http://eab.abime.net/showthread.php?t=50039
Since you have split the games across multiple partitions, other launchers and scripts won't work as they are designed to use one assign only - A-Games:, which points to one location for all games. You can manually change this in the scripts by adding a second assign for B-Games:
http://eab.abime.net/showthread.php?t=48711