The motherboard should detect the drive no matter what it's set to. The OS on the other hand may or may not understand AHCI or RAID, in which case the drivers must be installed during the OS instalation.
If you are using XP, set it to IDE. If set to anything else it will require drivers. Win 7 has native AHCI drivers and I believe Vista does too.
Are you setting up a new system? If so, put the drive on sata_0 of the main controller (assuming you may have more than one controller). If you are going to install XP, I recommend IDE mode in the bios. If it's windows 7, I recommend AHCI. Install the OS with just the one drive attached, other than the CD/DVD taht you will need to install from. After completeing the install, connect the remaining drives if you have any. If those drives aren't seen in windows, you will need to go into disk management and initialize the drives then they will show up.
I've only run into that situation once and it was a defective DVD drive causing the bios not to see the other drives. As soon as I detached the DVD player, all other drives were recognized.
If you move a drive to a new system and that drive has a windows OS on it, it will most likely not boot due to the fact that it won't have the necessary drivers installed for the new board. A clean install of the OS is recommended.
The sata ports may be numbered or labeled differently. The motherboard manual will show how they are labeled as well as it should be printed on the motherboard. The marvell ports are just additional sata ports as there probably wasn't enough bandwidth for the main sata controller to have more than 4 ports. If your board supports raid, the marvell controller may have been installed for raid capability.