Hey no worries.
I encourage you to experiment and discover your own methods as there really are no hard and fast rules. Some variation of these steps may help you.
1 Build a joint rig
2 Attach bones to joint rig (use whatever method you like)
3 Convert bone geo to ziva bones. Convert muscle geo to ziva tissues, and use attachments to connect the muscles to the skeleton.
4. Bake out your muscle simulation to an Alembic cache.
5. In a new scene, import your baked muscle cache. import the baked bone cache. Convert them all (muscles and bones) to ziva bones.
6. Make a fascia mesh and convert it to Ziva cloth. Use attachments/ collisions to attach the zCloth to the muscles /bones.
7. Bake the fascia simulation to an Alembic cache.
8. Make a fat mesh by projecting the fascia model onto the render mesh, and combining the two layers.
9. Convert the newly combined object to a tissue.
10. Import the fascia Alembic cache, convert it to a Ziva bone and drive your fat using attachments.
11. Wrap your render mesh to the fat bake. Usually people paint hands/feet/face back to the anim rig.
You can see there are three distinct simulation "passes" or phases. Muscles, fascia and fat. When you have the settings right for each phase, you can then switch out different Alembic Bakes for different shots.