You're asking about Android but saying the box is a Linux PC, which is confusing me. My answers are based on Android boxes, which I use. They may or may not be much good for Linux boxes.
If you have an Android phone then there are plenty of apps that will work as remote controls. If you want to use a PS3 controller, then it depends on what level of support your (Android) box has for PS3 controllers (if it's Linux then they should just work). Plug in the receiver and see if you can navigate the menus using the d-pad. If you can, you're good. If you want to map certain buttons to specific tasks, then you can use "External Keyboard Helper Pro" to remap the buttons. I have the shoulder buttons on my controller configured to control the volume, for example, and the red button to act as a mute. The only issue with this is that it will prevent the correct mappings working in emulators etc, and you'll need to find some way of switching the alternate mapping on and off. I've managed to do this as I also have a mini keyboard and have confiured alt-tab on that keyboard to switch mapping on and off for the joypad, all with External Keyboard Helper. If you only have one control method, you'll need to make sure you have shortcuts to the app handy wherever you may need to switch configurations.
