Disk numbers are not that important you can normally assign them by the order you connect the cables between the motherboard and the drive . The first Sata Port will be Disk 0 the second Disk 1 Etc, so may be changed around for aesthetics by changing the ports used .
In your case I suspect that the M,2 Card is hard-wired so always takes Disk 0
Your system should work fine as it is, I assume that you are using, or intend to use, the D: drive on disk 0 as a data store and run the OS and it's related partitions from Disk 1