For the windows on secondary hard drive bit, it's fine as long as you don't have it connected while installing on the primary drive. At one point I technically had 8 on both my HDD and primary SSD until I formatted it.
I probably wouldnt recommend touching anything on the HDD until you format it, just in case. But all you need to do once windows is installed is plug the HDD back in, start up the computer (make sure the SSD is before the HDD in the boot order in BIOS), go to disk management, and format the HDD. I had no problems with this.
I believe this might help you with your disc issues, give it a read and see where that gets you:
http://lifehacker.com/how-to-create-a-windows-8-installation-dvd-or-usb-drive-505769939