if you learn lets say the major scale in one key,remember to learn it on each string. This makes transposing it to other keys very easy as these relative shapes are just moved up and down the string. If you knew a shape for C major on the A string then G major on the D string will be the same shape moved a whole step higher.Make simple associations and when you are searching for the 3rd,b9th etc of any key center please remember the notes in a linear way on your favorite string and the 4ths will be on an adjacent one. The moment you find your favorite method to commit this to memory you will be at peace :). Hope this triggers some thoughts on stuff we honestly get completely befuddled with when we are with the instrument. Am sharing purely my perspective because this is how I rationalized the fretboard and came to some conclusions. You do not have to accept MY way but generate your own is what I'm telling you :)