One step at a time with lots of reinforcement. The notes on your page are literally a picture representing the shape of the music. Understanding music theory requires a fluency in reading notes. Many teachers and students use the shortcuts to reading music like FACE for the spaces on the treble clef. The problem is that there are multiple rules to reading each clef that frequently get confused, it is not a logical approach to see how everything fits together and when notes above and below the staves appear, there is no method of attack to figure out what keys to play.
In addition to doing the above, my students play by rote a great number of technical exercises by rote: trills, scales, 5-finger patterns (Ma/mi/dim/Aug), chord progressions, chord inversions, arpeggios and so on before we hit the concepts in the theory. All gradually increase in complexity and speed. I do Not hand out papers with the various things on them until we have gotten very complex as it is critical for the student to understand how to figure each thing out for themselves even in keys they have never done before. Between reading notes on the staff fluently and by Knowing how to play the theory concepts by ear & muscle memory everything makes sense. Then you Really understand the theory from the inside out.
Too many teachers present music theory as disconnected bits separate from the whole music. This approach makes it very difficult for students to find the logical progressions and leaps forward in understanding. Music and it's theory is Not bits and pieces of knowledge, rather a structured, homogenous whole.
I've had many transfer students who had never really figured out how the music fits together, but it is really quite simple! The Grand Staff that we hang all the notes on is really just a sideways keyboard! Each line and space is equal to one of the white keys in order! If you are using the Grand Staff with a Treble clef on the top staff and a Bass clef on the bottom staff (the standard configuration) a little short line in the space between them (a ledger line or essentially a staff extender) is Middle C - the C key closest to the center of the keyboard. If you know the names of the keys, you know that if you play keys stepping up(to the right) from Middle C, the names of the keys go forward in the alphabet: C, D, E, F, G, A, B, ... and so on. If you count each line and space from Middle C going up the letters are exactly the same. If you go down(to the left) from Middle C the alphabet is backwards. On the Bass staff, if you begin from Middle C and go down the letters of the alphabet also go down and backwards.
I make all my students learn the musical alphabet backwards (G to A) fluently. From the very first lessons we work on this. While the music is still simple and one note at a time, each student must be able to play the music and say the letter names aloud while they are playing and be able to play the music and count out loud in order to pass the song. We start the process by pointing to and saying the letter names aloud and by clapping/tapping the rhythm aloud. Doing this, plus the ever present music theory pages solidifies the internalization and understanding of how the music fits together