Designing topology

I’ve seen many examples of how to create topology for the human body, but I have not made the connection from there to how to design your own topology. For example, say I have an alien with a different body plan than a human, what principles do I need to know before I start designing the topology for it?

I think you are talking about Anatomy. Well for starter study the Muscles and Their placements at various bones & Joints. this gives a very clear cut picture for organic modeling.