One very important difference it makes: you MUST use the drivers for the RAID chip you have! I certainly would not use the jmicron drivers for a RAID controller built into a mobo's nVidia chipset.
Some boards have two different RAID and hard drive controllers provided by different chips. For example, my ASUS A8R32 MVP Deluxe mobo has a ULI Southbridge that provides the main SATA controller with 4 ports including RAID capabilities, plus a separate Silicon Image controller that provides a fifth internal SATA port plus an eSATA port and includes some RAID capabilities, too. Each has its own driver installed.