As far as wedges go, how do you know the rider's body is aligned correctly?

I could write a book about this question. For the sake of trying to keep this interesting (stick with a short reply) I will offer a link and give a short answer.

http://bikefit.com/whywedge.php

Here are two basic things to consider. How does it look and how does it feel.

Looks – generally you will pedal with your knee tracking closer to a straight line. Whatever movement (knee pattern) or deviation you had before wedging, the goal is to reduce the knee movement that may go from side to side or some other pattern besides straight.

There is one illustration of this in the link above.

Feel – This is generally felt with a more even or balanced feeling near the ball of the foot when clipped into the pedal. Please see the bottom illustration of the diagram in the link.

Hope this helps.