I wouldn't call it a "stupid" question; I remember the process confused me, but you'll soon get the hang of it.
Short answer: No, you do not need to have started your applications. Of course, though, you'll need to have created an account (which I'm assuming you already have). Your letters will get sent in, and they will be posted to your account. You'll be able to view who sent them, etc. once everything is processed.
Once, you submit your applications your letters will be sent with your report to the school; letters can be manipulated to be sent to certain schools, if you want to. I only had two letters, so I never specified anything, I just let them both be sent to all my schools.
Hope this answers your question.