Back when I was in high school, schools sent application packets to students by mail. Those packets included all the forms one needed to submit and some included a slew of envelopes that were labeled for each component. Regardless of envelope, everything got to admission offices by mail and got filed from there.
I wound up working in my Alma Mater's admission office and spent a good part of my year filing documents. There were thousands of documents coming into the office, but our little staff filed and filed to make sure all the components met up. We actually enjoyed the work a little bit...I even remember sneaking into the office with two admission officers (one of whom is now a counselor at a private school in Connecticut *wave*) one Saturday to finish the filing as a surprise to the administrative staff. The dean came in to garlands made out of envelopes strewn around his office that Monday. This is probably why I enjoy the days when we help open the mail here in the Office of Admission at UVa.
These days, the process is far smoother and doesn't take nearly as long. The Common Application automatically tags every document you send online with data that allows our system to file automatically.
Each night, the Common Application system sends newly completed applications (we have things set up so it only sends us your file when you submit all three parts of the application, the Common App, UVa Supplement, and payment). Our system runs a script (an automated process) that looks through any miscellaneous documents that have arrived by mail. If it finds a match, the system moves those documents from the miscellaneous area of the filing system to the newly created file for your application.
Items that arrive in the mail are scanned and loaded into the system for the same matching process.
No matter how your documents are sent, they will all meet up in the end. Some schools still have the traditional, paper filing system and that will work just fine (it will probably take a little longer than our automated system, of course). This is one part of the process I don't want you to worry about.
Once your application is processed by our system, you'll get an email confirming its arrival. That email contains your login information for our SIS (Student Information System). You can log into SIS to track your application (you'll see your checklist shrink as items arrive). You'll also see a link to your decision on notification day This is explained in the application instructions, which you've hopefully read at this point!