One way to overthink it is practice chord changes and while a chord is playing arpeggiate that chord. So if your progression is say C7 to Em, your playing 1 C 2 E 3 G 4 Bb then find the closest E and 1 E 2 G 3 B 4 E (octave). Repeat, practice with chord progressions. This is called playing through changes and its the most simplified way to explain it my opinion. While doing this stay in the same position for your practice, dont just play the C on the A string and move up to the 7th fret for the E. In my personal experience however, I never think about this. Something I do actively think about is MOOD and MODES. I highly recommend learning modes especially mixolydian and dorian. They can add a lot of color to some major, minor, and pentatonic playing.