There's no way to switch between 68000 and 68030 as the A3000 does not have a 68000.
Perhaps you're thinking of clicking the invisible close gadget in the upper-left corner on the boot screen to get directly into Kickstart 36.016 (i.e. the "tower ROMs")?
I know how to use both mouse buttons in 36.016 to select the Kickstart to load (either from HD or floppy), but my question is around how the MMU maps the Kickstart image it loads from disk - once mapped, is it persistent (i.e. survives reboots) or can you "re-select" each boot?
I was once told by an original ROM tower owner that, for instance, if you load SuperKickstart 2.04, the only way to get back to the menu screen and choose SuperKickstart 1.3 was to power off and back on before holding down both mouse buttons, but if that's the case, WinUAE isn't behaving that way.
Rodney