If the layers are predictable, then you can program them into the ConDoc Configurator to create your own drawing set. I made a handful of tutorials for this on the Learn Page.
If the layers are not predictable, you could use ConDoc LT. You will need to turn layers on/off before shooting your plan, section, elevation, and perspective scenes… but once they are created, you can continue to modify. Think of ConDoc LT as a jumpstart for scene creation and sending to LayOut, then you handle layer visibility manually.
Let me know if that gets you moving in the right direction…