If you have plants in the tank already, I wouldn't take out the plates because you will rip a lot of the roots. If you don't, then yea, take out the fish and remove them. Try to keep the gravel as thin a possible, the more you have, the easier it is for anerobic spots to for due to a lack of circulation. The less the better. Make sure you do have plenty circulation in the tank. What kind of filter(s) do you have in the tank? Do you have anything like a powerhead?