MSI NEO 4 Platinum with SATA Drive

I have recently built a new machine with the following specs but I am having problems with system stability in windows and was wondering whether it's because of the way I set up the hard drive.
Specs:
MSI K8N Neo 4 Platinum
AMD Athlon 64 3500 Winchester
Zalman CNPS7000B-Cu
1GB Corsair XMS PC3200 RAM
Sapphire X800 XT
Sound Blaster Audigy Player
Maxtor 80GB Serial ATA Hard Drive
Maxtor 40GB IDE Hard Drive
550W PSU
I plugged my SATA drive into slot 1 and booted from the maxblast 3 CD to partition and set up the hard drive. I then installed windows 98 and upgraded to windows 2000. My system seems to be slow and laggy, though it seems mostly fine in games. When I listen to music and browse a CD at the same time the sound stutters and lags. I am getting lots of slow down when doing lots of things on the computer but it shouldn't slow down as much as it is. I am also getting windows error messages.
Is there a different way I should have installed the hard drive. I can't boot from my windows 2000 disk in dos because it's only upgrade version. I read on the forum about adding the SATA drive to a raid array before installing windows but I don't understand what this means. Can you help?
The floppy drive also doesn't seem to work so I couldn't install SATA drivers at windows setup. How can I get it working because the lead seems to be connected correctly as it gives an error message on boot up with the purple stripe the other side of the floppy drive.

Quote
I can do it with a windows XP upgrade CD surely
yes
Quote
Me Yesterday, 12:55
If you have an XP upgrade CD follow the following steps.
1) Decide which HD you wish to install XP on.
If the Sata - Then turn of PC & unplug IDE Drive, this is a windows thing, as XP will see the Ide drive b4 the Sata & try to create the 1st drive as system drive. You can plug the ide back in when the install is complete.
2) Insert XP Cd. Enter Bios - Advanced bios change boot order so that CD is 1st device. or press f11 as pc posts, & select CD.
3) The PC should now boot from the XP CD.
You don't need to load any floppy drivers.
But XP will ask to see a qualifying product, put in your 2000 or 98 CD.
You should see a Hard drive Partition Setup screen - you can use this to delete any existing partition & format the drive (Don't use the quick format it's only quick cos it dont check for errors so slow & safe is best.  See section How to partition and format your hard disk by using the Windows XP Setup program

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    Quote
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    Quote
    Originally posted by Calculusaurus
    Quote
    Originally posted by ninjastyle
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