System pages mainly contain the content used in the ecommerce process, such as text that appears during registration, checkout, order confirmation emails, order/despatch notes and so on. It is also used on certain parts of the site, such as text that appears in the footer.
When you are setting up your ecommerce site, you will need to go through your system pages and ensure you are happy with the content. A quick way of doing this is to make a purchase as a new user and check that the default content is acceptable to you. Continue the order all the way through to completion to check the different email notifications are also acceptable.
You can edit the content via Page Manager in the System Pages section.