Like others, I found with my November 2013 purchased Mac Mini, Apple had installed the internal hard disk in the bottom location (bottom when working on the unit upside down as detailed in this guide).
I found that it was best to remove that drive, and install the SSD in the bottom location, but use
* 2 of the rubber grommets and screws (that came with the ifixit kit) on the front edge of the drive
* that let me use 2 of the screws from the original mac mini on the back top HDD as they are larger screws than came with the kit
That way the HDD didn't rattle in the top location.
* Installed the SSD in the bottom location with the original apple cable
* Installed the spinning 1TB drive into the top location (which made it easier for the top wifi screws to screw into
* But I had to reshape the cable (that came with the ifixit kit) quite a bit to get it to line up with the connector on the logic board.