Windows 7 has swapped my drive paths with my boot drive and sec. drive

The machine is running perfectly. I needed to have the HDD drives disconnected when performing the windows install. I had one snafu. I had the bios set to AHCI when I did the install, I figured that since only the SSD was connected RAID mode should be deactivated. After everything was loaded up, I powered down, connected the HDDs, powered up and changed the bios to RAID, and booted up to a BSOD. Sure I let loose a couple cuss words, but I didn't panic. A quick search on google and 15 minutes later everything was running perfect. All I needed to do was a switch back to AHCI in bios and tweek the registry.

Here's the change you need to make while in windows under ahci.

run regedit and go to HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Servic es\iaStorV

Change the Start REG_DWORD from 3 to 0

Restart into bios, change to raid and it should not bsod when booting up.

Credit is given to Medo145 from the Overclockers.com forum for this fix. It worked A1 on the first go.
Big thanks to everyone who has taken the time to help me out with this. Thanks :)

You mean AHCI : Enable in Windows 7 / Vista - Windows 7 Forums ?

May I ask why you want RAID for your data drives? File size? You do know that you'll most likely lose all data if one drive fails? Much better in most cases to have separate HD's.

Be sure to back up.

You can still post the Disk Mgmt screenshot if you want. We spot problems in about half of the tens of thousands of times we've asked for one.

My machine is mainly a gaming rig. It's my hot rod, and I like to tinker with my hot rod. I don't really do anything of great importance with it, any pictures or music I have is backed up on a ext. HDD. So if a drive were to fail it's no big deal. I enjoy fixing it, just as much as I like to play on it.
I know the risks of RAID 0, in my own opinion the key is to really take your time and research that drives you buy to use in this setup. My last system which this new one has replaced was built back in 2005, and it had 2 WD Caviar SE16 250gb drives in a RAID 0 setup. Never had a failure, data loss, or anything bad. They are still working 100% and are now being used as external hard drives. They're old and I don't doubt them one bit.
If I had something worth not losing, then yeah RAID 0 is risky. But it's my hot rod, and hot rods are built to go fast :)

Sure I'll post a screen shot.

How is Win7 faster when its data drives are in a RAID0?

Isn't it the SSD that makes it faster, not RAID0?

Well with my new machine, no raid doesn't help windows because the os is on a SSD. The SSD is only going to contain windows only. Programs, games, music etc. will be on the HDDs so it will help how fast games and programs load up. In gaming it will make maps load up much faster, load screens very short, etc. On my old machine the os was on the raid setup, and my boot up times were almost as fast as my SSD.
Look at it this way, RAID 0 is meant to share the workload among x amount of hard drives. So if a SATA3 drive works at 6GB/sec, then 2 drives in RAID 0 will work at a pseudo 12gb/sec.

Any programs installed to a HD will run slower than if they were installed on the SSD. I'd only offload User files for best performance.

Any repair or reinstall run while the OS drive is in a lower position than Disk0 risks derailing the boot files onto the first-in-order Primary partition. The solution to this is to have the OS in DISK0 position or any preceding drive's partitions be formatted Logical which cannot accept boot files.

Before I added on the HDDs, the SSD was marked as disk 0. When I added on the drives before raid they were marked as disc 1 and disc 2. After raid activation windows bumped the HDDs to disc 0 and the SSD to disc 1, why? Does windows favor the larger drive? Is it possible to bump the SSD back into disc 0 position? Just for clairity, what do you mean by "user files"?

For best performance what is your recommendation?

Sometimes Windows has its own mind about OS disk not disk 0 - Windows 7 Help Forums.
I don't think you can force it, just be mindful to unplug all other drives if you need to run Startup Repairs or Reinstall. Or you could convert the RAID to Logical if it allows it: How to set partition as Primary or Logical with Partition Wizard

Best performance is always having the programs on an SSD, moving only the User Folders - Change Default Location

Thank you GregRocker for your time and expertise. I used partiton wizard to turn the raid setup in to logical drives. But after reviewing our conversation regarding the pros and cons of raid. I have come to the conclusion that with the benefit of the SSD, which in all honesty is my first time experience using, that having a raid setup just isn't worth the trouble nor will I really benefit from it. So I have returned back to a AHCI setup with a single HDD in a logical format to be used as storage and I'll concentrate on tuning windows for max performance with the SSD.
Thanks again!