Can anyone help me with these queries?

I have just enabled AHCI support for the SATA (ICH9R) drives on my Gigabyte GA-P35-DQ6 motherboard. After a little fiddling around they seem to be working perfectly, however they will now not show/get detected within the BIOS screen. Is this normal?

Secondly, as I now have no way of knowing what controller they are on, is there any advantage to having my single HD and single DVD drives on particular SATA ports e.g. HD on SATA0, DVD on SATA2? And if so what would be that recommendation?

Thanks for any help.