You could buy a net to put it in... Or media bags. Or you could make a strainer so they stay in their compartment. Egg crates may have to big of holes but you could look into them. If you want to build strainers check out uarujoey on YouTube.
So I have an edge 6g with a crack in the top that I don't use looked over at it and got this crazy idea in my head that I am going to incorporate it into the system thinking couldn't I just use a lot of live rock in there and not have to worry with bio balls or the matrix Am I just crazy or would this work