You can add it as a semi transparent layer in FCP and render it out, or add it in something like Compressor or MPEG Streamclip at the end of the job.
To add in compressor, go to the inspector, filters tab, and choose 'watermark'.
In MPEG Streamclip as far as I know you can only add text, but useful if you want to add 'not for TX' or something simple.