This is hard to get used to. Really hard. But it is important, to try to smooth out the pedal stroke and take some of the work away from the quads. This – using the whole pedal rotation – is a huge part of the benefit of using road / mtb shoes.
So, the system I learnt, when first getting into training indoors is this:
[A] First, focus on the push, at the top of the pedal stroke, with the right foot. You should try to push your foot off the front of the pedals; when you do this, your toes will migrate a little [depending on how tight your shoes are] into the front of the shoe. Try to keep the force horizontal [Of course, there’s downward pressure from the quads too.] . Do it for 30 secs. Go to the left and focus on the push. Give yourself a break from trying to push – say a minute – and then repeat this.
Then focus on the pull, right foot only, for 30 secs. Now, try to pull the shoe back towards you. Your heels will migrate a bit into the heel of the shoe. Again, horizontal pressure. Take a break from pulling. 30 secs on the left foot. Rest and repeat.
On your first serious go at this, stop at this point and focus on the workout and power. [Remember that it is easier to do this when the cadence is low. So find a part of the workout where you can reasonable hold a cadence of 60 rpm, say.]
[B] Next time, repeat these two exercises. Then have a rest from them for a minute. If possible, increase the cadence at which you do the exercise, say by 5 rpm.
After a minute break from push and pull, do the push exercise again, but this time, trying to combine pushing right foot and pushing left foot [alternating, of course]. Do this for 30 secs. Then try to combine the pull right and pull left for 30 secs. Take a break from this focus for a minute and then repeat.
From now on in, you keep repeating these exercises in paragraph [B], each time trying to increase the cadence until you reach your preferred cadence, and gradually raise the length of each drill to one minute.
Then you can go onto the drills that Chad asks for in the workouts. But until you can do a minute at your preferred cadence, of combined right and left push, followed by combined right and left pull, don’t do the exercises that Chad is asking for. Gradually, you will find your pedal stroke becoming smoother, and the left pull / right push becoming synchronised. When it happens on the road: magic.