We have a step-by-step tutorial that describes how to skin your CMS Suite v3 website. See here: http://v3suite.dmxready.com/help-guide#8
Please note, the CMS Suite uses a single "master" template to render content from database. You can add database content or site components by simply adding the template files and or objects to your master template. This allows you to place things like your header, your navigation bar, your plugin apps, and your footer wherever you want on your page. See here for architecture:http://v3suite.dmxready.com/help-guide#10
You can also place your custom code directly on the template and use ASP (if/then/else) statements to show/hide content based on querystring.
FYI, If you are looking for help with installation and skinning, we also offer these services: http://www.dmxready.com/installation-services and this http://www.dmxready.com/product/pro-services-pack-2