Absolutely anything at all. Just make sure you have OS3.9's SetPatch running or you might get the wrong sizes.
I was using 3.5 to create partitions on my HD then installed OS3.9 and found out I was using half my HD and I'm pretty sure it was SetPatch - I cold booted OS3.9's floppy and got the full 20gig, but cold booting OS3.5's floppy gave me only 8gig.