Jose,
Both options should work. I would set up the assemblies the same way they are being built. I would use some sub assemblies.
Question, What's driving the sub systems locations (springs, Motors, etc)?
When you look at the pictures you would have to have a spring, linear motor system or something to drive the postions of the components as gravity would not allow the system to work as shown.
Need more definition as to what's making the parts move?
You can drive multiple motors in a mechanism analysis at the same time, just extend each motor definition time line to overlap each other (might look at a table driven motor instead of a graph driven or equation driven)
Hope this Helps,
Don Anderson