all over the fretboard

"Which way is the best way to learn the major and minor (natural) scale all over the fretboard so that it works out with the modes?"

"focus your understanding."

Study Music Theory ,

maybe prepare for a music theory exam .
By doing this you will be involved in written tasks which will teach you how the notes fall in place, intervals between each string and so forth .
Learn to sight read :

By starting to sight read music you will find the different positions on the neck to play the same note .
study for a guitar exam

this will introduce the neck to you in managable chunks, starting with one ocatve scales moving up to 3 octave scales , this practise schedule will focus your understanding of fingerboard knowledge .
I hope this is of help to you .
Best wishes damien