Good early morning from Australia!
My apologies, I was so busy last night fixing the site I didn't have time to repost with an update.
After much research and reading into the system, I finally wrapped my head around how it is suppose to work and how it is integrated in Joomla, and after this my question does sound indeed silly! I've removed the individual articles and replaced them with the corresponding menu types. Thank you for these awesome forums, the amount of searching I did and random bits of information all tied in nicely!
To help future people searching, there is the ability to add descriptions, images, custom modules and images into the category content this will allow you to have a custom product page, or edit the design of the product page to insert modules into the page - much the same as having an article and loading the products in - except the opposite, you will have a proper structure of products and load in the other modules.
For template design:
- For individual design elements simply edit the description of the category to include {loadposition position-} , can also add images. descriptions etc...
- For design changes across the entire view - edit the view