Setting up new hard drives

Nightingale1

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Dec 2, 2015
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I'm replacing my old hard drive with two new ones, a 250g SSD and a 1TB HDD, and had a few questions before I get started.
First off, I'm not planning on cloning my old one. There is little I need from it, and I know there are viruses in some of the files, so I plan on starting fresh. Can I copy the OS onto a flash drive and boot it from there, or do I need to find the original OS disks?(I know I have them somewhere, I just have no idea where)
Also, how do I control which hard drive is the primary storage? Is there any specific problems I should know about?
I'm sorry if these are dumb questions. I'm not new to computers, but I have never ran two hard drives at once, and never owned an SSD, so I just want to be on the safe side before i try anything.
 
Welcome to Tom's Hardware, Nightingale1!

I think that I can assist you with a couple of tutorials, that can shed some light on setting up your storage configuration (SSD & HDD). Good thing that you won't be cloning, because it would most definitely cause you issues (since you have malware/viruses).
Shortly, yes, what you want to do is possible. The OS communicates with the motherboard, so the activation lies there. You can swap the HDDs, but as long as the mobo stays the same, you can simply use the guide from MS about clean installing your OS version: http://windows.microsoft.com/en-us/windows-8/clean-install

As for the whole configuration and setting it up from BIOS, here's a step-by-step you might find useful:
Win 7 - http://www.overclock.net/t/1156654/seans-windows-7-install-optimization-guide-for-ssds-hdds
Win 8 - http://www.overclock.net/t/1240779/seans-windows-8-install-optimization-guide-for-ssds-hdds

Hope it helps. Keep me posted if you have more questions! :)
SuperSoph_WD