The only drive recognized where, Windows, or the BIOS?
What are you trying to do with the driver installation? Are you moving a system drive from another PC to the new board? If you need to install a driver on your system disk, don't connect your eSATA drive yet.
Also, if that board has hotplugging (which needs an AHCI driver) you don't need to have the eSATA drive connected when you start the PC.
You need to give us more information about what you are trying to do.