I’m a squid, but I found your USAFA appointee guidance. It’s very clear on how they want you to handle the initial security clearance. They even underline it. Lesson #1 in the military, if they ask for X a specific way, deliver X as directed. Or did you see something that made you think there was an option? That would be helpful in answering your question. Of course, USAFA provides phone numbers for every aspect of the instructions, including security clearance, so it would be easy to go to the official source to clarify if needed.
At some point, you will start using the eqip system.