I think I understand you but I am still abit confused.
I changed my step 6 to:-
6. I create my index.php page by going to Webassist> Framework> Themes > Create Page From Theme
7. I add my dynamic plugin pages to the editable regions on my index.php page using a url parameter $_GET['']
Now the next step I would like to take is to allow a user to customise thier page lets say for example change the font-color on the site how would I do this?