insert at the beginning of your s:startup-sequence (assuming you've got 3.1 installed to the "wb3.1" folder, but it can be anywhere):
if "$Kickstart" eq "40.69" ; change to appropriate version to check
assign SYS: SYS:wb3.1
CD SYS:
assign FONTS: fonts
assign L: l
assign LIBS: libs
assign DEVS: devs
assign C: c
assign S: s
assign T: ram:
execute s:startup-sequence
quit
endif
Been using 2.x & 3.x that way for ages on the same partition, IIRC even 1.3.