PowerCMS and the user registration uses different table name, so you should be able to just add the PowerCMS tables to the database that uses the user registration, you might want to try just running the database script that came with PowerCMS in the users database.
In regard to combining files and folder, i don't recommend that you combine the files and folders. Instead in your site create a sub folder for PowerCMS (CMS) and include the PowerCMS files in that folder, and then you can just have the user pages in the root of the site.
I hope this could help you in getting started.
