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Bass Song in Eb

My son and I are learning a pretty complex jazz song in Eb. We want to play via the notes, not tab. Considering new guys are learning, best to play the notes on the first 4 frets, and learn them really well? My thinking is that I can play any song, if I know these 16 or so notes on the fretboard.
 
It's good to learn the first 4 frets, sure, but not "best". "best" is to learn the whole neck.

If I were you I'd:
Find all the notes of the key Eb in those first 4 frets, with D string fret 1 as your "base," but also: find the notes of the key Eb based around the A string, 6 th fret and see how the same key functions in a different position.

If anything, I'd suggest positions farther up, that avoid open strings, as they tend to reveal the common "movable" fingering patterns more clearly, and can be better for learning the abstract patterns of music.

(Tho personally I love using open strings...gives each key a unique feel.)
 
... "find the notes of the key Eb based around the A string, 6 th fret" - yes, mambo, that was my first attempt - the song "plays" better at this position, more fun and sounds better.
 
Learn how to play the Eb scale starting with each of your 4 fingers for the "root" note, then you will be comfortable no matter what. :)

If you listen closely to the original you *might* be able to tell how the player is fingering it. Acoustic upright jazz players very often use the open strings whenever possible; if you hear the open strings ringing out then you can figure out the fingering from there.