A handy plugin to help with docking is NavBallDockingAlignmentIndicator. When you select a docking port as target, it puts a red circle on your navball. When you are pointed at the circle, your docking ports are facing each other. Then, with RCS translation (IJKL), you can move your yellow prograde marker around the navball. If you keep the purple target marker between the prograde marker and the center, you can 'herd' the target marker on top of the red circle. Then move your prograde marker on top of the other 2 markers and you're set. Hope that made sense. The plugin is a big help.