You have two different SATA controllers, AMD 6Gbs 1-6, P0-P5 in BIOS.
ASMedia 6Gbs 1-2, Po and P1 in BIOS
What's listed in Devise manager assuming you are using Windows? Under "IDE ATA/ATAPI controllers" you should have "AMD SATA Controller" and "Asmedia 106x SATA controller". These drivers are on the motherboard cd.
You may need to reassign priorities in the BIOS, it's under the "BOOT" section.
I have mine setup much like you do.
PO & P1 Raid0
P2&P3 Raid0
P4 hot dock
P5 hot dock
ASMedia ports
P0 Optical drive
P1 e-SATA
Speedbird 9590@5.1/CHVFZ/8gb G Skill@2133/ASUS R9-280X all on EK blocks controlled with Aquaero 6 Pro
Goonybird 8350@4.6/GA990FXAUD3/16gb Corsair@1600/Crossfired Sapphire 7990's cooled with CM 240L XSPC res