Hi Michael,
There are two ways that I have used.
1) Layout
Add parameters to your layout and refer to them in the assembly
and they will drive your assembly.
2) Family Tables
I prefer Family Tables. In your Family Table, instead of "yes", "no"
for whether or not you need that subassembly, you can enter an instance
name.
This allows for multiple configurations in the same model.
I built a top level helicopter that way before.
Sometimes we wanted to see the rotor blades drooped, sometimes straight.
Sometimes we wanted to what height the vehicle sat while fully loaded,
shipping, etc...
You need to play with it to get the hang of it, but it is all pretty
intuitive.
Best regards,
Frederick Burke