I am NOT sure about this, but it is my understanding that, if a SATA drive has been used (data on it already, etc) in native SATA mode, you cannot access it in AHCI mode. However, for the near term that is not a problem for you - the shop people didn't tell you the whole story.
Your mobo has 5 SATA ports, yes, but they are supplied / managed by two different controller chips. ALL of the ports should operate just fine as SATA ports. And it happens that one of the controllers can do IDE Emulation, and one cannot.
Any SATA drive can be connected to any SATA port. Then the port needs to be configured in the BIOS Setup screens, and there may be up to four possible modes. Basic "native SATA" - the port just handles it as a SATA drive. AHCI is a slightly more advanced port / drive interface protocol that gives you some extra features, some of which do not matter to many home users. RAID allows you to use the drive in a RAID array via a software RAID management system built into the mobo BIOS. Now, up to and including all versions of Windows XP, the OS had its own built-in drivers for using IDE devices and ATAPI, but NOT for these newer systems of SATA, AHCI or RAID. However, Windows Install utility did already have a way to deal with non-IDE devices for purposes of installing and running Windows - a step early in the Install routine that allowed you to load in external drivers you need for non-IDE units like SCSI, etc. So this method was available to set up a system with SATA, AHCI or RAID drives. BUT it only knew how to load those drives from a FLOPPY disk! And many newer systems did not have one.
The great solution offered by mobo makers and their BIOS writers was a fourth "mode" on the SATA port configuration menu: IDE (or PATA) Emulation. If you choose this, the mobo intervenes a bit and makes a real SATA drive appear to Windows to be a plain old IDE drive, and Windows is blissfully happy and ignorant of the deception. The downside is that making this choice means you do not get to use the extra features of true SATA or AHCI. NOTE that this still did not remove the necessity to load RAID drivers if you planned that, but that is was your problem to handle. And, if you actually wanted to use native SATA or AHCI modes, you still had to find a way to provide the drivers on a floppy during the Windows XP Install.
Next came Vista and then Win 7. They both added built-in drivers for SATA and AHCI modes (but not RAID), making the special IDE Emulation mode unnecessary. The also allowed loading external drivers from USB flash drives or optical disks, removing the need for a floppy drive even if you were going to install them to a RAID array to boot from.
So, in your case with older SATA drives containing data, the simplest solution will be to connect them to one of the first three SATA ports that DO have the ability to supply the IDE Emulation mode. Now, whether you need that mode, or whether you can simply use them as native SATA devices, depends on which Windows you have already installed, and how. If it was Win XP with no extra drivers installed originally, you will need the IDE Emulation mode to access those disks. If you have Vista or Win 7 installed, that probably can deal with your real SATA units in pure native SATA mode.
Now, when it comes time to use SATA ports 4 and 5, you will not be able to use IDE Emulation mode. I'm actually a little puzzled that the manual does not say they support plain basic SATA mode, but maybe they do. If you have Vista or Win 7 as your OS, they have the SATA and AHCI drivers and will be able to handle any SATA drive on those ports. If you have Win XP, you will have to install the SATA or AHCI driver in it to be able to use those ports - not a big problem, done within Windows just like any other driver installation. You will NOT be able to use those ports for a BOOT drive with Win XP because they cannot be made to look like old IDE drives, but that won't be a real issue for you.