it seems that you are applying your changes directly to the jsp pages generated by WebRatio. They are built using the model and style information coming from the project, so every time you generate WebRatio reads the model and style information and creates (or replaces) the jsp; that's why every time you generate you lose all your changes.
Here you can find more details about Style Projects in WebRatio: http://www.webratio.com/learn/learningobject/Getting-started-with-the-Style-Project
Here you have a tutorial with a section dedicated to Page Templates: http://www.webratio.com/learn/learningobject/create-a-style-project-from-a-mockup
Hope this helps.
Let me know if you need more details.