Usually when you do an install you do have to restart your cpu to get the OS to install. Why cannot you just restart and start the install into the partition? I also have a 2009 Mac Pro, try using another disc souly for the other OS, then install on that dedicated disc and when you start up, hold the option button in to decide which OS you want to boot.
Your system (OS) selection of where has to be done BEFORE any restart.
And you want to backup and retain a copy of the installer ".ESD" package first.
On restart it will self destruct the package.
A clean install on another drive or another partition.
I prefer to go with pulling the old drive.
Always retain backup boot ability and dual drive dual boot is just... safer.
If you're looking for an OSX installation disc, and, like me, you upgraded to Lion through the app store, you will have to go through a back-door process in order to create this disc. Here's an article on this. http://www.macworld.com/article/161069/2011/07/make_a_bootable_lion_installer.ht ml (I can't guarantee it works. I made a disc like this because I thought I needed it to reload from a Time Machine backup, but it turns out that Lion doesn't require the disc for this, so I never used it.)
When I installed Boot Camp and Windows, I didn't need the OSX installation disc. I'm not sure why you would, in this process. It should only ask for your Windows disc.
If for some reason you downloaded Windows from Microsoft instead of buying a package with a disc, you need to download the ISO version and burn it to a DVD. See this article on downloading the ISO: http://www.mydigitallife.info/windows-7-iso-x86-and-x64-official-direct-download -links-ultimate-professional-and-home-premium/ (Make sure you choose the ISO that matches the version you bought).
Here's instructions on burning an ISO with Disk Utility: http://lifehacker.com/251758/mac-tip--how-to-burn-an-iso-or-dmg-file-to-disc And this thread on burning a Windows DVD in OSX: https://discussions.apple.com/thread/2039118?start=0&tstart=0 (Summary: you can use Disk Utility to burn the ISO, but choose a slow burn speed)