Hi,
1) The payment receipt that you attach with your application contains a receipt number. They can see as to which fees you have paid through this receipt number. Many people pay the wrong fees, and CIC would check through this number and mail them to pay the required fees.
2) If you send your application to a PO box address you would not get a signed receipt of the delivery of your application from the courier service. While sending your application to the physical address would get you a signed receipt of delivery from the courier service. So its better to send it to the physical address so that you get assured that your application has reached at the right place.
Hope this helps.
All the best.