That depends on what your watermark is. If its just text, it can be as simple as creating a text layer, adjusting it to the desired size and position, and setting the opacity to somewhere around 15% (or whatever suits your taste). If its a graphic such as a logo, import the image into FCP and follow the same steps.
You can also apply a watermark using Compressor whenever you transcode or compress a file, say, into h.264 so you can FTP it or email it to a client for approval. Compressor has a menu to let you add a watermark at that step.
You can "watermark" audio by putting a beep in over the top at regular intervals: many apps that have a free demo period only allow saves and outputs like that until you pay for the software to unlock the protection. You can also have a phrase repeat over the audio periodically, instead of a tone.