Well, lets see...
First of all, do you have a floppy based copy of OS3.1? I mean all the disks, not just a workbench disk.
Also, when you boot from the floppy, can you see either IDE device? Can you insert the 3.9 CD and see it? If so, you should be able to set up the hard drive and install from there.
If not, you may need to copy an appropriate CD0 Dosdriver for your CD Rom to your bootable floppy. If you have a complete set of 3.1 floppies, it might be easier to simply set up the HD and install from the floppies, get your CD working and then throw 3.9 onto it...
Basically, as long as you can see your CD drive, you should be able to install 3.9 OK.
I only have 3.5 myself - you had to install OS3.1 first, then a pre-install for 3.5, then lastly a full 3.5. Perhaps 3.9 has a slightly simpler installation, I dont know.
