I like to keep my aquaponics drains a straight shot down (no bends or elbows). this minimizes pinch points (prevents clogs) and if it should get clogged (clay pellets, roots, etc) you can simply turn off the system and push any blockage up and out.
I also like to have emergency overflows
indoor units: on the elevated sections in case a clog prevents proper draining
outdoor units: on the fish bin - in case of heavy rain - don't want the fish swimming out
you can also look into DIY bell siphons that will drain and fill your grow bins (but they can be loud