At the ned of the day it all comes down to time an experience. You have your license you know know the theory.
As with anything theory does not all ways seem to tie up with the practical.
I used to live on the Isle of Man. Now this is a tiny island which is easy to navigate around on the ground, it is also fairly easy to navigate around from the air. Trying to pick out a specific village can be tough even on the Island. After a while it became easy. I flew quiet a lot with a well seasoned pilot who knows the Island from the air. He gave some cracking pointers on how recognise the various places from the air.
But all in all...time and experience.
Don't sweat it. As long as you know roughly where you are and are not busting airspace and know where you are going, you will be fine.