Going all the way back to 2005, I've always had a large strainer basket on the intake of my return pump. I have a few, so I can put them through a cleaning rotation. Originally, you could buy these at Savko, but these days that doesn't seem to be an option.
When I built my sump way back in 2010 for this 400g reef, I made a bigger bubble tower for the three drains. That seemed rather simple. Then later I added the 60g anemone cube that had to drain into the same spot. And I also added the biopellet reactor's output into that spot.
Back in 2013, I built my return assembly for the 400g version 2.0, and when I did so I used a check valve installed backwards, which I refer to as the Reversed Check Valve. When the return pump flows, water pushes the valve shut, but as soon as the pump has been powered down (intentionally or unintentionally), the backsiphon of water sucks the check valve open. When this happens I hear a brief sucking sounds letting me know the siphon has broken.