as far as the media goes depending on how many layers you have for it, i use coarse foam then slightly finer foam, into a polishing pad, then a big bag of purigen, and finally as much bio media as i can fit into it. if you have a good colony of bb then you will not need a ammonia reducer. you can put carbon in between the fine filter pad and the polishing pad if you want. i have found that carbon is not really needed in there. i used to use carbon all the time and then had to medicate the tank so i removed it. i never put it back in and it has been about 4 months ago now. for bio media, i have been using the fluval bio rings. i am about to try out the seachem matrix out. i found that pretty much any product that i try of theirs it the best that i have used. as for the intake and output placement, i place the tubes on opposite sides of the aquarium so in theory, you get the best circulation. the output tube if i am using just a regular defuser, i put it in the corner and face the flow were it is creating the current that you want/need. i like to make it so it causes a bit of surface disturbance to aid in your gas exchange. the spray bar, place it in the top of the aquarium horizontally. i like to again face it in a way that i can cause a good amount of surface disturbance to aid the gas exchange.