Hey Rusoloco73 - Sorry for the slow reply!
The team has been pulled in multiple directions this past week.
The approach that we typically take is to split our creatures into the following passes:
1. Bake the bones - we additionally bake the location of the character's root node to a locator during runup. This is so that we can constrain our solver to this locator in subsequent passes.
2. Attach the muscles to the baked bones and bake the muscles. (The muscles are solved as a zTissues)
3. Attach the fascia solve to the bone and muscle bakes and bake the fascia. (The fascia is solved as a zCloth object)
4. Attach a coupled fat/skin solve to the fascia and bake the skin. (The fat is solved as a zTissue, and the skin is solved as a zCloth)
For some additional flexibility, you could add an additional pass in which you couple in the render mesh (If it is different than your zCloth skin mesh)
Some suggestions for runup.
One of features of our software that helps to make it "production friendly", is it's ability to solve the creature relative to a coordinate frame. This frame is defined by the location of our zSolverTransform node.
During run-up, we will:
1. Solve the first frame of the creature in it's neutral pose at origin.
2. On the second frame, transform the character to it's start position/rotation/scale, by transforming the character's bones and the zSolverTransform node in unison. It's a good idea if the character's bones are grouped under a transform whose pivot is in the same location as that of the zSolverTransform node.
3. Ease your character into position over 10 frames or so - which will make your total run-up only about 12 frames.
Script the process - once your dependencies are established, you can then take advantage of Maya scripting interface for the purpose of automating the entire bake process.
I hope this helps!