1. After all orders Paypal send you a "notification of payment received" on your email address, the mail contain the name, and the content of the order.

To see the orders go to your admin panel ine the "customers -> orders" section. 

2. You will then see the listing of all the orders done on your website (an order done doesn't systematicly mean that it has been paid, please allways double check before send your order to the customers that he paid you via paypal, if note you can ignore the order). To edit / see an order click one time on it to highlight it, then a menu on the right hand side with the options edit, delete, invoice, packing slip appear.

One highlighted you can edit your order either in clicking on it a second time or either with the button "edit"

3. Editing your order: once an order has been paid via paypal and that you have received the notification of payment you know that you have received an order on your website.
Edit the corresponding order to see all the details, delivery address, billing address, full basket content and for your own organisation you can change the "status" of the order (second red box on the screenshot).

4. If you click on the drop down menu you will have different choice, Pending, Processing, Delivered, Preparing Paypal IPN / which is the default status.

Depending of the choosen option you can by this way organise your order and know which order has been treated or not. The status change in the listing of all the orders (see 6.)

5. When you change the status of an order you can decide to tell the customer, you can join a specific comment as well using the appropriate field (keep the tick box "append comments" ticked as well as for the notify customer), then click on "update".

The customer will then receive a generic email containing the staus of his order and your comment.
That option is very usefull if you want to notify you customer at each step of the order.

6. Once the status changed and back to the orders listing you can clearly see if you have treated / finished an order or not.

7. You can at any time see or print the invoice. You just have to click on the "invoice" link of an order.

8. Same thing for the pcking slip