Without seeing the system, it sounds like your free application has created an additional partiton on your new hard-drive. This is easily dealt with, however. Right Click on My Computer, and click on Manage. Once there, click on the 'Disk Management' option in the left-hand pane under 'Storage'. Your disk (C:\) should then be visable in the pane in the top-middle.
Click on it, and underneath you should be given a graphical representation of your disk. If the F:\ drive is appended to the C:\ drive, right click on that section and delete/remove it. You may need to use a 3rd-party partition manager to increase size of your main partition as XP doesn't seem to like that idea. I personally use partition magic, but I've seen some free solutions that unfortunately I can't remember off the top of my head.
Hope this helps.