Figured it out. If anyone else is confused by the instructions, what you want to do is create a transport route loaded up with fuel then when you get to your desired attitude (next to space station for emersion) DONT DOCK. Instead hit a button I think its called dump payload (or something similar) and dump fuel equal to the mass that would be delivered (kinda like token spaceship parts). Then you can either come back down and land or if that's not possible just stop the recording. Once this is done you will have a route with a cost and altitude associated with it which can be used to construct vehicles.
I think I like this system better than the other spacedock mods, anyway this mod allows you to automate other deliveries which is a big plus.