Looks like you cut into the 6". You didn't need to do that. All you have to do is sit the 3" on the top. You can flood and drain a 6" cube if you stack them you should feed from the top. You might get away with the flood and drain. Your roots will take and will be good for the full grow. If it was me i would feed from the top drain to waste. That way you are always flushing excess salts.