I now have Welcart working in a custom theme.
The "short" answer;
Copy the following folder
And place it in your new theme
DO NOT EDIT THE PAGE PERMALINKS FOR THE CART AND MEMBER PAGES
This will break the template usage. If you REALLY want to change the page permalinks you will need to modify the plugin core code.
This will now effectively allow you to style the plugins key functionality pages.
Next is getting the products out. By default I think it pulls them out into the blog.
The best way for me was to create a custom template page. This is a little more advanced but does allow you to fully customize the layout and output.
So I created a page "shop" and then had my custom template pull out all products/posts in the category "item". Then when someone clicked on the item in the list, it took them to the items individual page which was using the
Anyway, this is hopefully enough information for anyone who has the ability to modify themes and plugins. For anyone looking for a plug and play solution then this plugin is not really it. It is a great plugin, there are some bugs and annoyances, but overall is perfect for my current project.