You need to identify the 1st note of the scale in two places (i.e. the "c" note on the 3rd fret 5th string and the "c" note on the 5th fret third string. Use the "c" notes as anchors or bookends and play the scale within those frets. At first try to locate all the possible "c" notes on the fret board and then play the scale within the octave bookends.
After you have mastered that for a scale, select two octaves, and then three (use segovian scale fingering technique for moving up and down the fret board)
After you have mastered one scale (i.e. major) do the next scale. At some point you should be playing the scales anywhere on the fretboard.
The next thing you have to master is playing all the different scales in one octave location. For example, the "c" note on the 3rd fret 5th string and the "c" note on the 5th fret third string. Use the "c" notes as anchors or bookends and play all the scales within those frets (major, minor, relative minor, major pentatonic, minor pentatonic, all of the modes, etc...)
After you master all of the scales in one position for one tonal center (in this example "C"), do it for every possible key.
Another variation of these exercises is to sing the notes as you play them; sing and play every other note (play first note, sing 2nd note, play 3rd note, sing 4th note, ...)
I know this is a lot of stuff but it puts you on the right track to learn the fretboard, learn your scales, and develop your ear.
Good luck - this is a couple of months/years work!
