Docking can be one of the biggest learning curves in KSP. Here's how I first learned to dock massive ships.
Set your heaviest, slowest ship (the station) to align the port with the "normal" direction. Right-click the port to "control from here" and then let SAS slowly do its job. If you're in the usual eastward launch counterclockwise orbit around Kerbin, that docking port will be aiming north, and tends to stay north even if the rest of the ship rotates during orbit.
Next step is to rendezvous your heavy lifter with the station. Get close to the station, then slowly maneuver to be slightly "above" (north in my Kerbin example) of the station's docking port. Right-click to control from the heavy lifter's docking port, set SAS to "target", and let your lifter slowly rotate to align the docking ports.
Gently use RCS to move the lifter towards the station. Watch the navball and keep the yellow direction indicator centered. Regular docking ports like a speed around 0.3 m/s or slower, the klaw needs 1.2 m/s.
Note that if you switch control back and forth between ships, SAS mode may turn off or reset to heading hold. In my copy (heavily modded 1.7.3), SAS continues to work in the correct mode for the ship I was controlling, but resets for the ship I just took control of. Keep the station targeted on "normal" and the heavy lifter on "target".
All this assumes your docking ports are aligned along the centerline of the ship. If you have a radial port on the side of the ship, SAS aims at the center of mass rather than the ports, and you may need to manually point one or both of your ships to keep the target indicator and direction indicator centered.
I find 2 mods useful for docking. Better Time Warp (or similar) allows tweaking physics timewarp (Alt->). I set the maximum speed to 10x (default is 4x) so I waste less time watching massive ships align themselves. Just make sure to go back to 1x before actually docking.
The other docking mod is helpful for all docking, and essential for radial ports IMO. It gives a camera and a green indicator as things get close to docking.