SOS vs DOR registration
You would typically register with a Department of Revenue (or its equivalent) in states where you create nexus, and need to collect sales tax. Registration with Secretary of State (or its equivalent) is necessary when you establish more permanent physical presence in a state, for example by opening an office there.
I invite you to read this answer to a question dealing with nexus to better understand the difference. Not every state where you establish nexus necessarily requires you to register with SoS (this is also called "foreign qualification"), however some do.