You can change Windows 3/x Setup from MS-DOS by typing "setup" from the Windows directory. From there you can change the "Display" option to VGA.
You could also edit system.ini as noted. You would change the "Display=" line to read "Display=VGA.DRV"
Doing it with the first method will prompt for the setup diskette if VGA.DRV is not present in the Windows\System directory. the latter option won't show the prompt, but either way if it is not present you'll need to find the proper VGA.DRV file. (It should be present on any install, I'd expect, but stranger things have happened).