Also when you get close to the target ship - click on it's docking port and set as target. Right click on your docking port and select "Control from here". Now you just have to put pink target marker in the middle of navball and approach it. While doing so, you will have to keep that target marker centered. Just move it using RCS controls (IJKL). Works very well for me. I never used Mechjeb and I don't understand people who can't dock without it. Its very simple. The only glitch I had was when the pink target marker was not really pointing towards a docking port. It only happened to me once, but it was not that much off, so after ships got within couple of meters, I made some adjustments to make it work. Most of the time target marker is spot on, so no adjustment is needed. Keeping it centered on navball is enough. It works so well that I have no trouble docking in the dark. Docking ports have to be pointing towards each other though. Easiest way to achieve that - switch to a target ship, mark approaching ship as a target ant point your docking port towards it.