There are two ways to edit the Project Website. The first is by using the basic event software editing tools. These are accessed in Manage Project Website using the Edit General Settings and Edit Page Settings buttons. The second is by using the advanced Online Payments editing tools. These are accessed in Manage Project Website using the Edit Page on Website buttons for individual pages. Advanced Project Website edits should only be done at the very end of building your project. All of your initial work - particularly creating the right type of pages, publishing your packages, and choosing your registration settings - must be done through the basic event software editing tools. Once you're done building the basics of your Project Website you can move on to the advanced Online Payments editing tools using Edit Page on Website. If you switch back and forth between the two forms of editing you will risk overwriting and erasing your advanced edits.
Think of it like baking a cake. The basic event software editing tools allow you to build your initial site, aka pour the batter and bake the foundation of your cake. The advanced Online Payment editing tools allow you to make advanced design edits and add extra features to your pages, aka frost and decorate the cake. If you later go back and try to make a change to that foundation after you've already decorated the cake then you will mess up all that pretty frosting and will have to re-do it.