I grew up playing piano, so the keyboard is my reference. Years later, learning the fretboard has been less about learning which string/fret combination sounds a given note, but instead, given a certain chord:
1. where is the root of that chord, and with that as my anchor...
2. where is the 3rd, 5th, and 7th of that chord? Only once I can easily find those three intervals...
3. where is the 9th, 11th, and 13th. Finally, the sharps/flats of all of the above.
When it comes to organizing all of this across the fretboard, I've found the heptatonic approach to the fretboard to make the most sense and the most economical. YMMV.