Usually it is possible to see what the files are intended for either from a readme packaged with the files, or else just by the filename.
In any event, "DS9 cards" only contain two chips (PIC and eeprom) so there are only two files needed for any given card. If there are more files in the set you downloaded, then they are simply variants of the PIC and/or the eeprom file - perhaps intended for different receivers or CAMs, or perhaps with differing keys in the eeprom file.
A funcard is based on a different (Atmel) chipset than the "DS9 card". Depending on the software you load, which receiver and/or CAM you use, and which providers you want to zap between, you may find that one works better than the other. I find, for example, that the DS9 card is less reliable in switching than the funcard, but faster (with my FreeCAM2 in an Echostar DVR7000).
And note: "DS9" (Deep Space 9) is actually the name of the software which is most popularly used with this particular type of card. The card itself is normally referred to as a Silver card, or a PIC2 card.
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