Reinstalling OSX to new drive

I recently received a brand new shiny Mac Pro (thanks to AppleCare) after my G5 went belly up. It came with only one 500GB drive and 1GB of memory. I upgraded to a total of 5GB of memory and put in 3 additional 500GB drives. 1 WD SE16 for backup of main drive and two WD RE's striped RAID 0 for storage needs.
From the very start I was noticing problems. After starting it up for the very first time I got the dreaded spinning beachball. This was during the simple set up of the computer. After a minute of spinning I clicked off to the side and it finally came back to life, skipping one of the setup screens. Things seem to be acting very buggy. Safari has crashed. Photoshop has missing buttons. After Effects...don't even get me started with that. IPhoto has greyed out selections when it shouldn't be.
Now I know that After Effects has its problems. I've researched and realize I'm probably going to have to upgrade to CS3. But everything seems off.
I've run Apple Hardware Test (both regular and extended) and everything comes up roses. I don't know if it was a bad install of OSX or if somehow the original drive from apple is faulty.
I would like to do a fresh install (not a clone of the original HD) of OSX onto the WD SE16 and install some apps and see if there is a difference.
Can I just put the install disc in and tell it to install the OS to the WD SE16 without harming/erasing any of the other drives?
If I can do this is there anything I have to do to make sure that the computer starts from the correct HD?
I appreciate your time and input. Thanks.

Can I just put the install disc in and tell it to install the OS to the WD SE16 without harming/erasing any of the other drives?
Yes. Just be aware that you need to boot from the installation DVD to install to any drive, even though it's not the boot drive.
I can do this is there anything I have to do to make sure that the computer starts from the correct HD?
When it reboots after the installation it'll be set to boot from the drive it installed to. If you're concerned you can hold the Option/Alt key and manually select it but it'll do the right thing.

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    http://www.shirt-pocket.com/SuperDuper/
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    Hi,
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