AHCI or IDE for my 2 HDD's ?

Yes but I beleive your newer hard drive is SATA and it being either a SATA2 or SATA3 device you want that as your primary os HDD and games cause it will be faster in terms of performance over old IDE which is only ATA100 or ATA133. Plus you have to relize your old drive has probably been running for some time has some miles on it. Check and see if your motherboard supports what SATA version 2 or 3 and get back at me.

also read up on it here.
http://www.geeks.com/techtips/2005/techtips-010605.htm

Thanks for posting those links now I know exactly what HDD's your using, lol sorry I'm at work being to lazy to look them up. I see why you want to use the samsung cause it's 250gb and sounds logical for your OS HDD cause it's smaller, but look at the WD. It has 64mb of cache, and the samsung has 8mb. So go with the WD as your primary, connect both to your sata 3g ports and your good. And if you want the best bang for your buck in the future for an upgrade that you will really notice grab an SSD on sale, just grab a sata 3 (6g) and that way your future proof for your next build

In general with newer Windows versions, it is a bad idea to set a SATA HDD to IDE mode. Why? Because it MAY be slightly slower, and it eliminates a few new features that all SATA HDD's have.

It might help to understand why any mobo BIOS has this odd option for "IDE Mode". By coincidence, the new SATA system for connecting and controlling HDD's came on the market at nearly the same time as the release of the original version of Windows XP. That version did NOT have any "built-in" device drivers for the new SATA devices - more properly, they are AHCI devices from a logical perspective. So Win XP could not use them, and could not even install to them. Now, Windows had had for some time in previous versions a way to add drivers for "non-standard" devices like SCSI drives and RAID arrays as part of the Install process in such a way they the became "built in" and fully usable for that particular installation. (That process still exists and is useful in some cases.) It involves loading the driver from a floppy diskette early in the Install process. (Later versions of Windows expanded this to allow loading from USB sticks, but not in Win XP.) But many people were building new computers with no floppy drive, and they were stuck! So BIOS and mobo makers included a neat work-around to allow people to install and use Win XP on SATA hard drives. In the BIOS where the SATA ports are configured, there is an option chosen on a line for "SATA Port Mode". You can choose things like Native SATA or AHCI, but another choice is something like "IDE (PATA) Emulation". In that mode, the SATA controller on the mobo does NOT use any of the new features of SATA units and makes the OS believe it is using a plain old IDE device type. Windows XP DOES have a "built-in" driver for that device type, and it is happy to Install on and use such a drive that appears to be an old friend - an IDE device. Thus, users who had Windows XP in ALL its versions had both choices available. They could use the BIOS IDE Emulation mode for simplicity, or they could set it to proper AHCI mode and do the driver Install from a floppy as part of the Windows Install process.

All this became quite unnecessary with Windows VISTA and later because Microsoft included an additional "built-in" driver for AHCI devices in all of them. Thus with these Windows versions there is absolutely NO need to use the IDE Emulation work-around in BIOS. There is no advantage to it, and you lose some features like hot-swapping capability and command queuing if you do.