C:\\WINNT\\ is usually the directory that Windows 2000 gets installed into. This is because Windows 2000 is based on NT technology and they didn't change the default System Root directory.
Nero, IIRC, only supports one CDRW drive at a time. You may have to switch the Recorder drive under the "Recorder" menu or just press Control-R. That was with Nero 5.X, Nero 6.0 may be different. Also Nero has the license to only use the drive type it was shipped with. So I assume it was shipped with the Yamaha, but not the Sony, and the registration code is for the Yamaha only. You may need to purchase a new serial registration code to use both drives. Email them first, maybe they can make you a deal with the new Nero 6.0 upgrade to cover both drives?
If Clean! is like Nero, it depends on the serial number as to which drive it supports. You may not have a valid serial number for either drive. In that case it may only support burning to the virtual drive which creates ISO images.