CommonApp Online or Paper?!

<p>I am a bit confused by this whole submit online or paper process.
I recently sent in a paper version application to one university for Early Action.
If I am sending in applications to other colleges for the regular decision deadline, is it okay if I submit those applications online via commonapp.org or do I have to print out everything and send it in separately too? And since I already sent in one application by paper copy, do I have to click anything on CommonApp to show that I have sent in my application by mail?</p>

<p>Thanks!</p>