Reading music is one way to learn the location of notes on the fretboard.
Yes - working on incorporating that as well. Fortunately, I can read music - took piano lessons in elementary school - but just never bothered to transfer the knowledge to the guitar or bass. Tablature ruined me! I took the easy way out and am definitely a "rock bassist" in many ways. Time to get back to it!
I know I tend to play (and think about the notes) from the roots on the lower strings up toward the high strings. One thing that I found useful for working on learning the notes on the upper strings is to play from the root on the high strings down to the low, this is also a useful exercise for working on improvisational skills.
I use all four fingers on my left hand to fret and like to play from the position where the roots on the low strings fall under my pinky, especially on a five-string since low tones are still available high up the neck on the B string making it easy to stay in one position and play across the neck instead of up and down. When playing with the root (or any other note) under your pinky on the B or the E string the octave will be three strings over and fall under your index finger so another easy way to learn where some of the notes are on the D, G, or C strings.
Both of these are great! Again, I have almost always taken the easy way out - playing only the patterns that came naturally or that felt comfortable. I've occasionally approached things with the pinky on the root on the low B, your post inspired me to incorporate it - it makes a lot of sense and opens up patterns that I have never used!
Playing down from the high notes makes a lot of sense too - I played with that a little today. I'm learning some of the F#s! C# is next on my list...
I need to learn this too; I'm even too ignorant for 5 string-if I'm not looking down at an E string I am lost...
For me, I've been playing in ignorance of the notes for so long, it's hard to even realize what I don't know! I've been a pattern player most of my life - it's not necessarily a bad thing, in fact, I think it's a valuable skill and I am still able to make music, but I'm realizing that I want to take my music further. It's slowly happening!