Double-installed Windows

Afetr a major glitch in Windows 98, I decided to re-install. But in order to retain as many settings as possible, I installed into a folder within the existing Windows folder (C:\Windows\1). I think I found the missing files in the original install, and transferred them across from the new install. But now of course the PC always boots up to the new install.
How can I make it boot up to the old one, and will it be possible to delete the new one ? Any help much appreciated. Thanks.