great question-
yes, i could probably write volumes about this in this post, but let me share with you some key things that really helped me out when i was trying to get a handle on this...
to me, learning the fretboard is more about your ear training and intervallic awareness than anything else. the reason for this is that the bass is tuned symmetrically, and musical shapes and componentry layout the same on the instrument, regardless of what the key center, scale, arpeggio, etc, is... (of course, not all of us are playing basses that are symmetrically tuned in 4ths, but the intervallic and ear training applications still apply in these instances.) understanding how the layout of the fingerboard is 'mated' to what you conceive/hear is the key.
in my observation, by far the biggest problem that plagues most bass players (or most stringed instrument players, for that matter) whether they are aware of it or not, is that they play more with their
eyes than their
ears. in other words, they depend more on the rehearsed shapes and patterns to navigate the fingerboard than they do an actual, spontaneously heard/inspired idea. the irony in this is that we typically practice patterns and shapes in order to learn the fingerboard better...

however,
once we reach the point of tackling the muscle-memory challenge embedded in each pattern, then we experience
diminishing returns with respect to true musical development. why? because we then transition from the 'learning' state into a state of "executing rehearsed repetitive motions", we reach the end of our learning capacity with those respective shapes and patterns. it is for this reason that i have in my studies and with my students essentially redefined the purpose for patterns... they should be used primarily as introductory muscle-memory development exercises, but
once you have them under your fingers, they need to be used exclusively for ear-training exercises, instead.
ok, so before i extend this into a book here, let me interrupt myself and make my main point. mastery of the fingerboard comes when you have the ability to hear something either internally or from an external source, and then play it immediately on your bass, without the need for any other reference or translation. it's the 'george benson' example... being able to spontaneously play what you sing or hear. all of us should be doing that all the time, whether we are singing out loud or not. this ultimately suggests that possibly one of the best ways to learn the fingerboard and how to navigate it is to work on your ear-training... and... one of the best ways to work on your ear-training is to work hard on transcribing music you hear, or at the very least, learning these things note-for-note on your bass, including all of the nuances of the players' phrasing, dynamics, etc, etc. this way, you are now having to
find the shape of the sound you hear on your bass, that would have been previously unfamiliar to your hands, because you never played it in that way before!!! so the ultimate goal then becomes:
be able to hear any musical idea and play it on your instrument spontaneously without error.
sound difficult??? well, sure it does. and it's going to take most of us a lifetime to achieve that... BUT, it's not an issue of difficulty...
it's an issue of unfamiliarity. so in order to make the unfamiliar familiar, we have to begin to practice a different way. not just play modes and arpeggios in all keys up and down the neck!!! that is not going to help us achieve this goal. keep doing that for your dexterity and facility on the fingerboard, but realize it's more of a technical exercise than anything else. start spending more of your time learning how to play what you hear without any assistance from a pattern or notation or youtube video, etc, etc.. unlocking the fingerboard means uncovering the music there by having to
FIND it.
ok, well i had no idea i was going to spend that much time on my answer, but there you go.
a couple more points that will help you:
-a lot of players don't realize this, but if you want to learn your fingerboard really, REALLY good, then you also need to practice your READING. i repeat... PRACTICE YOUR READING. reading forces us to find the notes (remember that word.. 'FIND'?) on the fingerboard that match the pitches indicated. of course, the greater range covered in the piece of music you are reading, the better you will progress. don't just practice reading basslines in the lowest octave of the bass.
-if you haven't done this already, get intimately familiar with the shapes of all the intervals on the bass. most of them have at least 2 locations that you can cover for the same interval from a single hand position.
finally, if you want some direction as to how to get started with solid ear training using your bass, check out my ear training articles on bassmusicianmagazine.com:
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whew... i'm tired now!!!!!