Not sure what you're talking about here. If you mean should you run these programs from your external drive, I would say no.
What I would do is clean up and de-infect your C: drive, then image your C: drive. Install the 80GB drive as your main device and then restore from your image to this drive.
I haven't used Ghost, but I have used R-Drive Image which will create the image and restore disk from within Windows and write it to DVD, or another drive/partition.