| where did I put that canned response? oh yeah, here it its...
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I'd say the logical progression learning music theory is this:
1.) Learn the major scale, and how it's constructed
2.) Learn how basic chords are built from the major scale- e.g Major is 1,3,5, minor is 1,b3, 5, etc.
3.) Learn how to harmonize the notes of any diatonic major scale by building chords / stacking thirds.
4.) Learn arppegios/chord tones
5.) Learn to look at common chord progressions as "numerals" (eg, I-IV-V ect) to understand how the chords relate to the song's key.
6.) Learn the Natural Minor scale (a/k/a Aeolian mode) and the dominant scale (a/k/a Mixolydian); And learn how these relate to the major scale (i.e.; its the V and vi mode)
7.) Understand how other 4 modes of the major scale are derived (less important to memorize these other modes at first)
8.) Dive back into modes for more detailed ideas about what "goes" with what chord.
And to expand on the first two points above...
I. Do you know the major scale- that is-
A. You know the whole-step and half-step formula for making a major scale
B. You know how to figure out the notes in any major key, using the correct enharmonics
C. You know what it sounds like- you know what the next note will sound like before you play it
D. You can find it and play it over two octaves ascending and descending in any key
II. Do you know how to build the basic chords- that is, you KNOW
A. A major chord is 1 3 5
B. A minor chord is 1 b3 5
C. A 7th chord is 1 3 5 b7
D. A minor 7 is 1 b3 5 b7
E. A major 7 is 1 3 5 7
F. A diminished chord is 1 b3 b5 bb7 (and you understand why it's called the bb7, not the 6)
G. An augmented chord is 1 3 #5
III. You understand and know the chords that come from the scale when you harmonize it- that is you KNOW not only that the chords are:
I Maj7
ii min7
iii min7
IV Maj 7
V 7
vi min7
vii min7 b5 (or half-diminished)
BUT, you know WHY!!!
IV. You can work out how to play the arpeggio over two octaves ascending and descending the chords in any key. You don't have to memorize them (heck, I hate memorization), but you can figure them out and they make sense.
V. You know how a ii V I defines a key center
Bass playing is basically a matter of knowing what to play over various chords. It may seem daunting at first, but my practical experience (bass in pop/rock) has been that I mostly use Major, Minor, and Dominant 7 related bassline patterns, usually based on chord tones and pentatonics. Even if you're playing some guitar oriented riff-rock, each riff is going to imply a chord of some kind.
"BUT HOW DO I APPLY THIS THEORY TO MY PLAYING?"
85%+ of the time, you will be going from root note to root note as the chords change. The trick is learning how to do it with a groove and feel that is stylistically appropriate to the song. The best way to reach stylistic understanding is to learn songs you like and pick them apart to see how the bassline relates to the chords. I cannot emphasize this idea enough: The answer to this common question is to LEARN AND ANALYZE BASS LINES BY THE MASTERS. Once you undertand what Jamerson (for example) did with a particular set of changes, these ideas become added to your tool set, to use, change, blend and create your own voice. | 
