You could solve everything at once, but to maximise iterations so you can get the right performance out of your muscles I'd still recommend solving the muscles separately in their own pass.
For the second simulation pass, just make a fixed attachment from every vertex on the fascia to the fat. You can just select the fascia cloth first, then the fat, and create an attachment.
Turn collisions OFF on the fascia cloth
Turn collisions ON on the fat tissue.
Turn collisions ON on all the underlying zBone objects. (your baked muscles and bones from the previous simulation)
In this case you're just using the functionality of rest scale/pressure on the zCloth (fascia) to pull the fat tight over the muscles/bones.