Hot damn... thats some fast program you have. It took me a long time before I even got to the moon, let along had enough confidence to try Minmus. And interplanetary stuff has only been very recently, pretty much when I started this thread. The SSP (Scotterius Space Program) is far more ambitious than mine.
As for docking, it involves a few things. Similar orbits then waiting until a reasonably close approach (<10km). Then you make your speed in regards to your target down to zero. Then gradually burn directly towards it. Then only docking is required. Be careful about docking ports as the 'Clamp-o-tron' and the 'Clamp-o-tron-Jr' won't match each other.
Finally, the best single mod I can suggest is MechJeb. It has nifty autopilot functions to take the boredom out of launches for the umpteenth time at a frame rate of like....5 when you have mega constructions (at least on my computer). But much more importantly, it has a whole range of information tabs that allow you to more easily finetune your flights. Knowing to burn up and down to change the orbit inclination (polar vs equatorial orbit) and more easily holding prograde when you want to focus on the map and not the navball....useful. And the close approach readout is VITAL for organising an aerobraking manoeuver in the Jool atmosphere from 100 days out.
Speaking of Jool aerobraking. I used this just last night for my most ambitious acheivement. I stuck a plane on top of a rocket and flew it out to Laythe, one of Jools moons. This moon has an oxygen atmosphere and so can handle jet engines. Enjoy the view. (if the forum doesn't cut the rather wide image down.)
EDIT: I believe that the moon in to the left of Jool there is Vall, one of the other moons. Truly a lucky shot.