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I have three systems:
Can I explain my base system with one stage in an independent claim and explain the additional stages of the base system in further dependent claims?
For example, starting the dependent claim as: "The method of claim 1 either has no stages or in the case of adding an additional stage, the method also comprising:"
In general yes, that is what dependent claims are used for. However, the base system in the independent claim will need, on its own, to be patentable. Also dependent claims add elements/constraints/specificity to the claim they depend from. If "either has no stages" means that claim 2 has something less than claim 1, that will not fly.
Separately, you may be mixing apparatus claims ideas with method claim ideas. If stages are physical things it is incomprehensible to say "method of claim 1 either has no [some physical thing". The "device of method 1" might not have a stage. But a method, itself, has steps, not physical things like stages. Of course those steps can be actions of or upon physical things. And some method claims may involve steps related to different physical things than other steps do.
One way to not require configurations that would narrow your claims more than necessary - could be wording like "after flowing thorough stage FGH, directing the flow through a pipeline of stages that include at least an ABC stage and an XYZ stage in any order." "After flowing through stage FGH" does not say "directly after flowing through stage FGH". You can do it without indicating that there are no stages between or besides your named stages and not indicating a required order if no order is required.
Another approach is to use a, b, c rather than first, second, third and state that no order is implied that is not specifically defined.
Think about the difference between apparatus claims and method claims. Sometimes there are no patentable claims to the apparatus becasue it is old or obvious but the method by which they operate together is patentable. If you get claims to a physical thing, the maker of it infringes. It is fringes just sitting on a self. To infringe a method claim one need to make it perform the method. In some cases it is only the end user who sets the method in motion.
Another thing to think about is divided infringement. So far the Supreme Court says to infringe a method claim a single entity (and possibly other entities under the control of the first entity) must perform all the steps in the claim.
