Which Eheim filter do you have?
I have the Pro II 2128, Ecco 2234, and Ecco 2236. You are supposed to put the blue coarse pad on the bottom tray, then ehfisubrate or ehfisubstrate pro over, also on the middle, and part of the top tray. Leave about an 1" or on the top tray and then put the white fine pad on the top.
The blue coarse pad traps large debris, the ehfisubtrate or ehfisubstrate pro allows for beneficial bacteria to grow on, the fine white pad traps the finer particles.
Another thing is nice to use is an inline heater. Hydor makes an inline heater, which connects to the output tubing of filter. Having an inline heater prevents fish from getting accidently getting heater burns and you don't see the equipment in the tank.