So I’m watching Pat run up and down the neck like a mad man and think to myself he obviously can’t be thinking about what chord he’s playing over. I can kind of understand like when I play blues I don’t have think, but of course I’m basically playing pentatonic so not much to think about. I guess I just can’t conceive how this works at that level. Maybe because after you do it a million times it’s automatic?

Just like playing blues. You can add patterns, scales, and arpeggios. There are books with jazz patterns that after learning you can use to connect the dots ie. notes. Some patterns, let's say the ii-v-i will start out as a scale or arpeggio, but with added inside, outside, chromatic notes it becomes more fluid sounding. So it becomes second nature to them. I've been told that before every gig Pat sits by himself and just goes through scales and arpeggios for a couple of hours. Then does his show!