Hi there,
I don't have your board or a Samsung M2 card but I am, running a Z97 Gigabyte board with a Plextor M2 card in the slot on the motherboard.
If I understand things correctly the M2 slot on your motherboard will only run at PCIx2 speed (the same as mine) but the Samsung card should be backwards compatible and should run OK.
I haven't set up a RAID array on my system but from previous experience I would probably install the M2 card and not attach any other HDD's at this time.
Go into BIOS, under peripherals/SATA Configuration and set the SATA controller as RAID. Disable the PCI M2 SSD RAID mode. Then install the OS onto the M2 drive. Don't worry that the SATA Controller is set to RAID as the OS will install in AHCI Mode.
Setup Windows by installing any hardware drivers that are missing and install available updates from Microsoft.
Once that phase is completed shutdown the PC and attach the drives you will be using in the RAID Array to the SATA ports. Restart the PC, go into BIOS and follow the instructions in the User's Manual for setting up RAID.