I did a similar thing with my mun mission, I had a command ship with a lander docked to the front of it. This pushed the lander to where it needed to land, detached then refuelled at the mun space station. The lander had landed, scooped up all the science and was waiting for the command ship to reconnect, share science and the quest went on it's much more fun to set up a reusable mission like this because you are constantly thinking of what happens next. If you add mods like KAS, Kethane and the excellent TAC Life Support, you end up with some highly complex and entertaining missions!