To use store credit, you'll apply it in the Payment Info section (Step 3) of the checkout process.
If you have a store credit balance available, the option to use store credit will appear above the credit card and PayPal options. Just check the box and the store credit amount will be automatically deducted from your order total.
You can check to see if you have a store credit balance by going to your account, clicking on "Store Credit and Gift Cards".
If you have store credit available, it will look like this: