Ok here goes with my first question!!

I am currently working on a media filled bed system ( flood and drain) and I am a bit confused about what happens to the fish tanks as you flood the grow beds. If say you are using a ratio of a 1.1 meaning the grow bed water volume is the same as the fish tank water volume as you flood the grow beds and they become full wont that empty the fish tanks and be a problem for the fish?
I have a very simple system no sump or filters etc as of yet. Should I have these in my system?