I have my 4.0 partition first on the hard disk (1GB) and my 3.9 partition second. They have priorities 3 and 2 respectively. When I want 3.9, I load Media Toolbox in OS4 and change the priority of HD0: (the OS4 drive) to 1, and then reboot (remembering to hold down Ctrl-Amiga-Amiga for a few seconds so it flushes the OS4 out properly).
It'll then boot into OS 3.9.
When I've done with 3.9, I go into HDToolbox and change the priority of HD0: back to 3, and reboot. Hey Presto, back to OS 4.
(Remember when you're choosing to boot OS3.9 from the early-startup menu (which can be done), the first thing it does is call SetPatch and reboot. Hence you still need to go into the early start-up menu a second time. If you change priorities as above though you don't need to worry about this.