The new version of the Catalog app makes it easy to manually reorder Perch Shop products.
You click on ‘Reorder’ and drag and drop products in the same manner you reorder other things in Perch such as Pages, Categories and Navigation Groups. I posted a video demo on Twitter.
To display the products on your website in the same order you define through the Catalog app, you need to set your sort options:
perch_shop_products([ 'sort' => 'productOrder', 'sort-type' => 'numeric', 'sort-order' => 'ASC' ]);
You can download the app from here.