I'm just recording a series of 3 video lessons on this exact topic as we speak. I'll let you know when they're uploaded.
I recorded one lesson on the fretboard notes yesterday that ended up at over 50 minutes after editing so I'm splitting it up and re-recording That just shows how deceiving this topic is.
I'll try and give you an idea of what I'm covering to try and help you out with this.
The first thing I do is start from the very beginning with learning the alphabetic sequence of natural notes: ABCDEFG and also tones and semitones (whole steps/half steps). You just need to know there is a semitone or one fret between B to C and E to F. Then it's a simple case of running through that sequence of notes on the A string from open to 12th fret. Just as a primer.
So then the 1st Method is just a case of learning the natural notes at the fret markers.
E string (3rd, 5th, 7th frets) G A B
A string (3rd, 5th, 7th frets) - C D E
D string (3rd, 5th, 7th, 9th frets) - F G A B
G string (5th, 7th, 9th frets) - C D E
You can then add the open E string and 1st fret F to give you quite a usable set of notes. The vid lesson covers accidentals at the start so you can then use that knowledge to work out the sharps and flats from these guide notes.
The exercises then involve sticking to a single string eg. GAB on the E string and playing through a sheet of these notes, randomly written, one note per bar to a metronome/drum machine/foot tap. That should seem almost too easy as you finish a full page. I'd love to develop an app that can just randomly display flash cards of customised note names for this test.
Next move onto the A string notes (CDE). Test until nailed and too easy. Next combine E and A string. Test until nailed and too easy. Move onto D string etc. etc.
Method 2 then uses this same test principle but applied to particular neck positions. I use two positions to cover the neck up to the 12th fret. Low position is frets 1 to 5 and open E string (no open A, D or G). There's a C major pattern in this position giving all the natural notes.
E string - EFGA
A string - BCD
D String - EFG
A string - ABC
Go through the same test system as used in the fret marker method.
Once nailed, add the sharps and flats.
Next move onto position 2 which is the 7th fret to the 10th fret.
E string - BCD
A string - EFG
D string - ABC
G string - DEF
12th fret is a repetition of the open strings so you can go through the exercises again an octave higher but there's probably no point because by this time you should be pretty competent.
The final exercise I use is going up each string playing the natural notes from the open string to the top fret on your bass and back. Then do the same thing with every fret (every note) and use sharps on the ascent and flats on the descent.
As practice material I'm going to include a load of different chord progressions to play through.
Phew. Hopefully that should help a little. If not then the videos will be on Youtube and www.talkingbass.net
in the next few days. I'll let you know.