Use and IF THEN ELSE combination on the Version command.
Would look something like (assuming you have 2 directories in the root with different versions of Workbench, probably obviously lots more than this but)...
If Version = 34
Then Assign SYS: Workb1.3
CD Workb1.3
Else
Assign SYS: Workb2.0
CD Workb2,.0
ENDIF
execute s/startup-2 ; you would have a different startup-2 file for each version
Loadwb ; Optional, you cold do that from within the s/startup2 file
endcli ;
.
The version numbers is wrong, it will be a value returned by the Version command. But that's a rough idea of how you could code it, in AmigaDOS.
SYS: might not like being reassigned in that way - it is a shorthand for "disk you have booted AmigaDOS from". Even with the assigns removed, it should still work.
I suspect it would be more complicated than that, as you would have to reassign L, DEVS, LIBS and C as well, to point at the right root directories, and you might have to force reload Libs, Devs and L drawer as well (I think L and Devs are forceloaded when AmigaDOS starts up, which might end up with the wrong versions being used on the OS you are switched to.
It is way easier with Sideways ROM on an accelerator, but that means a reboot if the OS is pointing at the wrong boot area. You might have to adopt a similar method.
