I'd partition the drive with the Amiga, then with WinUAE copy the whole CD from disk to a second partition, in a folder if you'd like. I believe copying the Emergency Disk folder's contents from the CD to a bootable partition on your 1200's hard drive will get it up and running and then you'd be able to run the install from the other partition.
Another trick, once you've gotten 3.9 up and running, if you want to run the boing bags they ask for the original 3.9 CD, you can get around that by simply assigning "AmigaOS3.9" to the folder you put the OS3.9 CDs contents in.
It's been a couple of years, but I believe this is how I did it.
