I'm trusting the system. Just keep playing scales and sooner or later, it'll hit me.

Separate your playing/practice time from your theory time. Read and write your theory without holding your instrument. Then once you go back to playing, you might have absorbed the theory better than doing it all at once. And it's always helped me to absorb concepts better to not just read something but WRITE it down. So if you want to learn a new scale or mode, just take some blank sheet music and write it. Then you have some good notes to go back to without opening a book. http://www.blanksheetmusic.net/

I am a slow learner, but I finally figured out how to know which note is the one, three and five, complicated, and not getting easier. But I enjoy the challenge and learning experience.
Sparks

What Steph said kinda makes sense. I have a workbook on scales and modes, and it encouraged using blank fretboard layouts to learn where the root notes in each position, in all the keys were. It was very informative, but i didn't stay with it. I need to get back to that, it's very valuable, kinda boring, i would rather play, but there has to be balance to learning, and these excercises do help in learning the fretboard.