It's simple, first you remove the faux plate around it with a flat head screw driver. You might want to use some cloth to put around the screwdriver to keep you from scratching it. Then, You will see three screws holding the stock radio in place. Remove these with a phillips screw driver. Once you remove these, the stock radio will slide out. At this point, disconnect the wires from the back and you're set.
Removing the cupholder just makes it a bit easier to pop the face cover off (faux plate). It kind of gives you a starting point at the top edge. And then you'll find 6 screws (3 on each side) holding the radio up.
One tip with the radio though, you may want to either pay close attention to its corners, edges,etc or place some masking tape over the other plastic in that region (the black to left and right come to mind). I kind of put a couple scratches/gouges in unintentionally while rough-housing with my head unit :-/.