When you're a beginner, well through intermediate player, one of the most frustrating aspects of learning is the sense that the fretboard and the logic and patterns of music seem so mysterious and you just can't see how all the pieces fit together.
I've found that one of the most helpful ways to deal with that confusion and overwhelm is to do what I call “thinking intervallically”. Intervals are the space between pitches – I suggest you work at analyzing scales, chords, melodies, arpeggios, really everything with an intervallic analysis.
This approach is commonly employed by many of the best musicians. After some time of doing this, the fog will begin to lift and suddenly, the dots will start connecting.
Here are some examples of what I'm talking about: A Cm9 chord is built of a root, min3rd, 5th, flat 7th and 9th ( C - E flat – G – B flat – D ) = that is an intervallic analysis. A minor blues scale is a root, flat 3rd, 4ths, flat 5th, 5th and flat 7th. A Dorian scale is: root, 2nd, flat 3rd, 4th, 5th, 6th and flat 7th.
Another way of using the approach of thinking intervallically is in relation to chords, for example, take one of the most rudimentary chords, an open C major chord. (third finger on the fifth string, 3rd fret, second finger on the fourth string, 2nd fret, third string open, first finger on the second string, 1st fret and first string open) the intervals from low to high are: root, 3rd, 5th, root, 3rd. You should analyze every chord you play this way, it will do wonders for your understanding.
It requires a good bit of discipline but I recommend you build up to eventually ALWAYS know all the intervals in EVERY scale, chord, etc – it's absolutely worth the effort!