You have two options for file uploads:
1) A page on your site where users can go to upload files not associated with a particular product/order - Create a custom page. Create a form that contains a file upload. Add the custom page of the navigation of your site. You will be notified via email when a user submits a file on this page. Here is a sample of what this might look like: http://www.myownprintshop.com/page/file-upload
2) Add a file upload to a product detail page - Go to Sites > [site name] > Products. Click the pencil icon next to the product name to open it for editing. On the General tab scroll down to the "Upload Fields" section. Use the form on the left to create a file upload for the product. After clicking "Add" the form will appear in the list of current upload fields on the right. The file upload size limit is 1 GB or 2 hours. Files uploaded to the product will appear in the "Files" tab of the order in your admin area of Pressero.