There are a few options when you start using Maya Muscle to set up skin deformations.
While you can start by creating bones and muscles and weighting to them, it is recommended that you do a more typical pass at rigging to joints/bones/capsules first. This lets you focus on getting proper weighting and transitions all over your rig so that when you create and add weights to muscles, you can transfer from each joint as needed.
This workflow is described in more detail in the steps below.
Step 1: Set up basic skin deformation for your rig
To set up a rig for basic skin deformation
When you are finished, you have a basic skin setup with joints/bones, and you can go on to create muscles.
Step 2: Set up muscle deformation for your rig
To set up a rig with muscle-skin deformation
Step 3: Create a cache for faster playback
When you are finished with the muscle weighting, you can create a node or file cache so that you can easily playback your animations and light/render more quickly. See Create a cache.