Your main Shop page will only list the tags entered in the Tag 1 field for all products shown in your Shop; you can think of Tag 1 as being your main Shop "departments". Clicking on any tag will then list all products with that tag, along with all those products' other tags. Clicking on any product will list all the tags assigned to that product.
You can customize the order of products in your E-junkie Dashboard under Manage Cart & Shop > Shop Preferences, where you can "pin" products up or down to move them to the top or bottom of your Shop listing. Pinned products will be sorted by the order in which you pinned them.