Well, in order to use your device as an remote first thing you are going to need is making sure that your device supports Infrared Blaster or IR Blaster. Until or Unless your device doesn't support IR Blaster you will not be able to use you device as an remote. If you're sure that your device supports IR blaster then head out over the Google Play Store and search for an remote app over the store. Once you get that install it over your device and all done you can use it to control your setup box with your smartphone.
PS: I don't think having a USB stick is going to make any difference with the IR blaster those are two different technologies having two different paths.