The order your products appear in in your storefront is the same as the order they are displayed in in your Admin Panel. If you go to the "Products" tab you can reorder them by clicking and dragging on the icon to the left of the Product Name.
Any new products you add will automatically be placed at the bottom of the list.
You can also change the order products appear within each collection. To do this, go to the "Products" tab and then click "Manage Collections". Click into the collection you want to edit and then click and drag on the product images at the bottom to move them around.