you create your scenes, then go to USER tab... Up top is "User options" put all channels to Auto mode. This will, Bellow, set all of your faders to Auto... Now, you can go to, say strobes, and click on the channel changing the mode from auto to LTP then to HTP then back to Auto. If you set the channel to LTP, you can now assign a midi or key assignment to that channel. The assignment will take priority over the scenes. You have your scene running, press the key assigned, the channel will go to full (independant) of the scene... acting like a flash button
You are correct, the trigger will only key the first step in a scene. The program was never designed to do step by step triggering. Only scene triggering. Due to that being a more advanced feature, i dont see there will be a change in this set up.