Like others have said, there is an app. Prior to the app (and still available), you would scan both sides of the check and email the images.
They also have a deal with UPS that allows you to go to a UPS store where they swipe your ATM card, scan the check and process the deposit. It's free. I believe the UPS method is the only one available to USAA bank customers that are not eligible for the insurance products. It's not too bad. There are a lot of UPS stores and their hours are at least as good as most banks.