I put mesh bags on the bottom of the sump, where its convenient to grab them when they get full of gunk, as long as they are in line of flow it doesn't matter. and I do not get bubbles doing it this way.
I also put bio media in towers, that if constructed right, will fractionate out DOCs
the one above is sitting in a 75 gallon sump.
I also plant some sumps to help reduce nitrate
below is a planted sump
same sump during a water change
the 75 gal sump again
I put containers of substrate, old bio wheels at random, so If I want to start a new tank, these things are available eliminating the need to cycle the new tank.
and a filter sock on a line to the sump
the above sump had 5 tanks running to its 5 socks.
I also put intermediate sumps in windows for marginal plants
I never like to restrict my options, and have even used a 1500 gallon pond for a sump on outdoor tanks.
below video of a bio tower fractioning out waste, on a pond
koi pond fractionation