Set one to 2, and leave the other alone (defaults to 1024). When both containers require all the cpu, Plex will basically take it all, and only leave the tiny fraction available for handbrake. But, you also have to remember that all containers by default have a priority of 1024, so, assuming that Plex wants it all and another container wants it all, and handbrake wants it all at the same time then Plex and the other container will both split the CPU down the middle and leave a tiny fraction for handbrake.