Allen, If you are using a Micro-Trak yield monitor, Farm Site will format the data cards. For Ag Leader and Case IH, I believe that you actually format the cards with the yield monitor itself.
With the Greenstar (John Deere) yield monitors, you must use their software to format and read the cards (Farm Site can read the data from your hard drive after you use JD Map to read it from the PC Card).
I hope this helps! R. Scott Nusbaum Farm Works Software