Integrating the two halves of your musical brain

Here’s a learning topic that I’d like to hear you expound upon:
How to get the two halves of your musical brain working together at the same time.

Here’s what I mean by that:

I’m an intermediate mandolin student and, in a typical daily hourlong practice session, I spend about 30 minutes on technique and theory, and 30 minutes on repertoire and on the next tune I’m trying to learn. In the technique and theory half, I’m diligently playing scales and arpeggios, reviewing my double stops, learning the fretboard, etc. It all makes sense and it gets more fluid and comfortable over time.

But when I play actual tunes in the second half, all that knowledge seems to fall by the wayside. I tend to fall into just putting my fingers where the notes need to be for whatever break I’m learning, letting my ear and muscle memory guide me along. But I lose any sense of what chord I’m in, where that chord’s root tone is, or what my arpeggio or scale options might be from wherever my fingers happen to be at the moment. I feel musically illiterate in the heat of the moment and seem unable to access all the stuff I know.

My great goal at this stage in my playing is to always know, any any given moment, what chord I’m in and where it is in the chord progression. And then, building on that, knowing where the root tones within reach might be so that the scales, arpeggios, etc., appear in my mind’s eye like landing lights on a runway while I’m playing. So I know my goal, but I can’t seem to work out exactly what specific practice techniques would get me there!

I should mention that I have your Mandolin Treasure Chest and in the past 2+ years I’ve been playing, I completed Master Class and often do the drills in Training Camp as part of my theory & technique practice. I also tend to mix it up a bit, though, also using Mike Marshall’s Arpeggio Workout DVD or his Fingerbusters book, as well as some double stop exercises I learned from Sharon Gilchrist..