Well, E1 and E2 are not Intel controlled ports, so you'll need specific drivers for those, they are really just extras offered on your mobo, avoid them if you can. SATA 1 and 2 are 6GBb/s (SATA 3) and 3-6 should be 3Gb/s (SATA 2). With a 7200RPM HDD you really won't notice too much of a difference between those two standards but I'd recommend putting your drive into SATA 1 or 2 anyway. And also, is your drive actually SATA 3 compliant? A lot of drives are still only SATA 2.
Wherever you bought it from should have it on the spec sheet. Or you could look up your exact model number on Seagate's website. If you really want to have top notch speeds, however, you're going to have to look into SSDs. A standard HDD isn't going to cripplingly bottleneck your system in any way, but a SSD would certainly pair well with the rest of your high end components.
1) Your marvel controller may be disabled by default and you would have had to go into bios to enable it - NOT sure, but you should check, if not using it and it is enabled then disable it until need - You probably will not need as you have plenty of Intel based sata ports. I know windows 7 has native support for Marvel controller, not sure if vista does, if not you would have to use the "F6" load additional drive during vista install.
2) Have a feeling you did not go into bios and verify/set intel controllers to AHCI and here again not knowing the default it may be set to IDE which would decrease the performance of your HDD. Also, downstream if you decide on getting an SSD if in IDE mode You will need to change to AHCI and if HDD was set up with ide mode, again headache.
.. Check your bios, if in ide mode, need to correct. DO NOT simple change it, as you will NOT beable to boot to windows. - Somewhat easy:
FOR Windows 7 but should be the same for Vista. Quote
1.Exit all Windows-based programs.
2.Click Start, type regedit in the Start Search box, and then press ENTER.
3.If you receive the User Account Control dialog box, click Continue.
4.Locate and then click one of the following registry subkeys:
5.In the right pane, right-click Start in the Name column, and then click Modify.
6.In the Value data box, type 0, and then click OK.
7.On the File menu, click Exit to close Registry Editor.
added - Reboot and go into bios and change to ahci.
On windows 8.
.. Some think it's the best thing since sliced Bread - NOT SO SURE, tried it and deleted it from system and threw disk in trash!!
It looks like a great operating system for tablets as an alternate to apple.
The feedback that i'm seeing is that "corporate" buyers do NOT like and probably will not switch over to.
Bottom line here is wait untill you see a Windows 7 edition with FREE upgrade to windows 8.
NEVER buy a New OS untill it's been out for 3 -> 6 monthes (Do NOT go by RC beta versions)