Fix Website -- 2

The guy who created my website has created the collections as "Automatic Collections". I want them to be "Manual Collections" so I created some and added products to it. However the products dont appear on the right spot on the Website. I need the collection section to be sorted out properly so that when I add a product to the right collection it appears properly on the website as well. Example: If I add a Men's T-Shirt into the shop I want it to be available under Men, T-Shirt and if applicable, New and Seasonal. Addtionally, when you are on the homepage and see the different products, there is a 'shop all' button. I want that button linked to the actual product. Note: not all products collections that you can find on the website are available right now. So the collections can be created in Shopify but should remain invisible until I have them in the shop. So far I have: Men's T-Shirts, Men's Hoodies and iPhone Covers. The other product collections will follow later.