Why not format the old HD? That way you start with a fresh clean new HD.
If for some reason you do not want to format the extra drive, you can set windows to only start the install that you want so that it does not give you the prompt.
set the default operating system to whatever and then uncheck the "time to display operating System" check box
I guess at this point you could just delete the windows folder and the users folder and the programs folder and so on. Keep in mind this is not the HD that you booted off so windows will let you do anything you want to it. It will let you format it or whatever.
Again i would copy all important data to the new HD and then format the old HD and then copy all the stuff back. That way important stuff is on both HDs. If one dies you still have your data.
just built a new rig. Installed windows on a fresh HDD, using the old hdd for data and stuff but the old windows is still on it, promting me every time i boot to select OS and taking up space
how can i remove it properly without formatting?
First off - remove the old install from the Boot Options by opening MSCONFIG - going to the Boot tab - selecting the old entry - delete - Apply (this removes the prompt to select the OS to boot from)
Then delete any files that you want to delete after you make sure any that you need have been copied to the new HDD (may want to wait a few days before deleting just to make sure you did not forget to copy anything you need from it - unless you need the HDD space right away !)
hmmm i had previously problems deleting windows files from other windows my suggestion is do what JDFan told about boot options then boot pc using some linux live cd like ubuntu and delete all files and folders.