Last stage contains all the engines on the main craft: Do Not Stage This!
The 3 stages before this are unguided rockets, keep this in mind as you use the last launch stage.
All staging before this is the launch stage and works normally.
Guided missiles are located in the outer racks and require you to right click on the docking port to decouple them. Once detached press the [ key to switch to the missile. You will have to manually add a stage before you can stage the engines on missile. Use weak bursts from the main engines and RCS to steer clear of the ship.