How to make sure directions on navball correspond to directions I see my ship flying?
Solution 1:
You could try using the Chase camera mode:
The chase camera view is relative to the craft itself and rotates along with it as its attitude changes; it may also be repositioned manually. "Up" for the chase cam is based on the orientation of the part the craft is currently being controlled from (usually the command module). This view can make docking much easier to perform without switching to docking controls.
Even with this, I think it would be better to learn to direct yourself using the navball, using the velocity indicators to see which direction you need to move to: find your retrograde marker and use RCS or thrust until it is pointing directly up. You can use RCS in the direction where the marker is in relation to the vertical: If retrograde is left of the vertical, use the left RCS (j), if it is below, use the down RCS (k)...
Solution 2:
Eyes on the ball!
This is one of the most important aspects of any kind of flight. Don't pay attention to what your ship is doing, pay attention to what your nav-ball is doing. While you may be inclined to use RCS for stopping horizontal motion, I find that it's sub-optimal at best. The available acceleration is often too low for any amount of horizontal motion that would pose a danger during landing. If you do want to use RCS for landing, you can (and should) still use the nav-ball, remembering that the controls are basically reversed: you want to thrust towards the retrograde marker, not in the direction that you want the marker to move like you would for the prograde marker during docking.
Instead of using RCS, use your main engine(s) to push your retrograde marker onto the zenith point (straight up) when starting your final descent. This should typically be about 100m-500m above the surface, although very skilled players will do this lower. Once there, your only job is to keep it there while you reduce your vertical velocity in accordance with your current altitude. Make corrections by looking at the nav-ball, not at your ship. The only reason to look at your ship is to judge your actual altitude, not to judge its attitude.
As far as using MechJeb, yes there are tools to make landing easier. Obviously there is the auto-lander. This is more than a bit cheap, though. Another option is to use the Translatron. In the keep vertical speed mode, you can set it to kill your horizontal speed while also keeping a specified vertical speed (for instance, a hover or slow, 1m/s decent). Other options with MechJeb, as well as some other plugins like Kerbal Engineer, is to display the current surface horizontal and vertical velocity. When landing, pay attention to the horizontal velocity and make sure it doesn't become too large.