You and Jeff are right. It is crucial to know the chord tones before getting into the use of modes.
I took probably a couple dozen or so lessons when I was first starting on bass at age 12-- about 18 years ago. Sort of learned enough to get going. My teacher tried to explain the circle of fifths and such, but he was throwing things out there that were way over my head. Either he was doing something wrong--- or it was me. I stopped the lessons when i felt I wasn't getting anything out of them. It turned into me bringing in songs, he would listen and help me figure them out. I eventually realized I could do this on my own. At this point I knew major and minor scales, and how progressions worked.
I've put in tons of playing and jamming hours since then, and was actively gigging for many years. In High school I faked my way thru 3 years of Orchestra, as I never took lessons in school, couldn't sight read and didn't know anything about DB technique. EDIT- just remembered I did take a music theory class in High School- the band teacher pretty much left us on our own to "learn" with some crappy old computer software while he tended to things more important than us. I didn't learn crap in that class.
Of course during all this time I figured out what chord tones are by ear. I knew the R,3,5 seemed to have more weight/strength in the character of a chord than any other scale degree.
So by ear, or by being told what the chords are I didn't have any problems playing "the right notes". On occasion I would be surprised when something like the 7th of a major scale wouldn't fit over a major chord- so I would ask "What notes are in that major chord you are playing". After being told I would realize "oh its major chord but the 7th is flat for some reason". I knew how to accomodate that.
So I've got a lot of the chord tone knowledge through experience, now I am just trying to make sure I know all of the names of the notes I am playing while I am playing them. Not just their relationship to the Root note (which I always know). I'm backing up and seeing how what I already know fits into music theory. The theory part is helping me tie my pre-existing knowledge back together into something more cohesive and meaningful.
I personally think I am ready for studying modes and what their place in music theory is. Based on what I've told you guys- would you agree?
Ryan