The following is a workflow overview of how you can build and work with muscles using the Muscle Creator window.
To do this, switch to the Edit tab and bend the actual bones/joints that the muscle is attached to into the Rest, Squash and Stretch states, then click the Set Current State As buttons for each state.
The way to think about this is the muscle goes through some centerline. That line is an implicit spline defined by the red boxes for Rest state, or the Sq or St curves for the Squash and Stretch states. You need to tell the muscle what state is what first, then fix or adjust those after storing the states. You must set all three states in order for state reading to work correctly.
Adjust the cross sections for each state for actual shaping. This is similar to custom muscle shaping, except it is all exposed and you have the exact three states you want. You can also put blendShapes or rigging on the cross section curves.