I order through the Earl of Sandwich Mobile App all the time. You just go directly to the pick up and let them know you're picking up a mobile order. The app does have options to Substitute cheese, meats, and adjust sauces as well as indicate special instructions.
On a discount note, you can apply promo codes in the mobile app (like the current $2 off Holiday Turkey on Thursdays) but you can't apply Magic Key Discounts.