The simplest way is practice and application, really. Its hard at first, but the more you do it and use it, the deeper it becomes ingrained into your memory and ears.
Practice and application on my instrument (guitar). I practice my scales everyday. For chords, I practice sightreading songs. Working on rootless chord voicings. You just have to do it, everyday until you can spit out chord spellings and scale degrees without even thinking about it. I suggest finding a sheet with all the chord and scale formulas and practice spelling them in every key until it becomes second nature.