You can download templates to design offline by selecting "Templates / Upload" from the main drop down menu. From there you can choose the format you're interested in. Once you navigate to that product page, you'll choose from one of the three icons to download your template from (PDF, PSD, Ai).
When your design is finished, come back to this same page to launch the design tool by clicking personalize. You'll upload each PDF like a photo and then drag & drop onto the appropriate panel. You can preview and interact with your design in 3D to see how the panels line up with each other. A PDF Proof will be available in your shopping cart once you click the RED "Save & Exit" button.