In FusionPro, in the composition dialog, there is an option "Output to multiple files". Try using this option to create a separate PDF or PostScript file for each booklet. You can also create your own naming convention, as shown in this thread (http://forums.pti.com/showthread.php?t=3375).
Next, create a hot folder for your printer with print settings for saddle stitched booklets. Konica Minolta should have software available for setting up hot folders. Basically, any file dropped in the hot folder gets printed. You may need to setup postscript printing instructions in your FusionPro template and output to PostScript instead of PDF, depending on how your hot folder is setup. Konica Minolta can help provide the specific PostScript commands for your printer.
Last step, copy all the booklet files into the hot folder. They will all print!
Hope this helps!