For dual-channel operation, you should use this arrangement:
Slot 1 (closest to CPU): Empty
Slot 2: RAM
Slot 3: Empty
Slot 4: RAM
You might be able to get the system to run with the RAM in slots 1-2-4, but it won't run in dual-channel.
If it was me, I'd put two sticks in slots 2-4 and sell the third stick. Or return the whole kit for refund and get an 8GB dual-channel kit. If you really need 12GB, buy one 2x4GB kit and one 2x2GB kit so it'll all run in dual-channel.