If you've enabled (via the setup wizard) EVERYAwards to award points for orders, but aren't seeing points being allocated to your customers, ensure the order has been marked as paid.
EVERYAwards will only award points on orders that have been marked paid. Any orders pending payment will have points awarded for them as soon as the order status is updated to "paid" from within Shopify.
To automatically set all orders as paid, you can login to your Shopify account, go to "Settings > Payments" and find the section for "Payment Autorization".
Here, select "Automatically Capture Payments for Orders" and click "Save".