Both filters will be seeded and working. When the time comes to clean, you clean one, and leave the other for a couple of weeks so your cycle isn't compromised. Plus, you get the advantage of better water movement, which unless you keep fancy Bettas, is always welcome.
This being the internet, there's always someone who will chime in and say filtration is the devil's work and no one needs that, but for 95% of fish, that doesn't hold up. A good filter does two things - it provides a good medium for beneficial bacteria and archaea, and it provides good water flow.