My teacher thinks that indeed we need to know the fretboard by heart, no thinking involved, just recognition. Forget the rules, and the numbering, we don't have time to count the frets when sight reading. The best way to learn the fretboard by heart, is by doing, that is by playing a lot of music in all tonalities and all positions, easy music I mean. The more you play, the better. He said: just do Sagreras books 1 to 3 and you will be fine. Sagreras will teach you a lot of patterns used everywhere, the very building blocks of music, he said. After that, you see them in your score you play them, see... no thinking, no counting frets, no memory games. I am by no means there, but I can attest that the Sagreras books are wonderful material too teach the fretboard.