Disk Numbers are assigned based on your motherboard ports and which port the Drive is plugged in to.
So other than changing the port you attached your drives to, that won't be possible.
When your BIOS loads it starts from Disk 0 and steps through each Disk number until it finds the disk containing the OS to boot into, so for example, if you had three Disks 0, 1 and 2 and it was Disk 2 that had your Windows OS while the other two disks were for backups or something else, it'd take a little longer before Windows booted up. However, you are talking milliseconds here, so I'd not be overly worried about it; although technically its best practice to have a single OS setup, with the Operating System plugged in to port 0.