Assistance with Shopify Collections

I am trying to move an existing Yahoo store to Shopify and am having problems deciding the best way to keep navigation close to the same. The existing site has about 21 main categories with each one of these having 1-12 sub-categories listed under it. So the main category page only has images and links to sub-categories, no products. Sub-category pages actually show products. The Shopify pages/collections are confusing for me. Help me figure out the best way to setup the new Shopify site. Should all the categories become collections? Or should the main category be a page with sub-categories being collections? You are the expert let me know. I need to know how to do this myself for future work on the site, so to complete the project you will need to send me a doc with step by step instrcutions on how to set this up, including the steps to add the items to the links/navigation on the site. This needs to be very clear, with each step layed out. If it matters we are using the Retina Montreal theme with shopify. If you have read all the instructions and think you can handle the job, PM your ideas and I will send you the url of the existing site so you can see the current structure.