Sounds fine to me.
In the Fluval externals, the water goes down through the sponges first to remove any debris, then starts to come up through the baskets towards the outlet hose.
Biological media should be the last media that the water passes through in an attempt to keep it as clean as possible, so having carbon on the bottom, then ceramic rings above is correct. You also have 2 baskets full of bio-media, which will help.
The 205 may be slightly small for your tank. It pumps 680 litres per hour giving you turnover of 3.8 times. The 305 would have been my choice for that tank, pumping 1000 litres per hour and giving a turnover of 5.6 times.
That shouldn't mean that you have ammonia which won't process though. 3.8 times turnover should be adequate unless you start to overstock (e.g. malawis etc etc).
Crushed coral shouldn't affect it either. I don't think your filter, or the set up of your filter is to blame for your lingering ammonia readings. I'll have a look at your other thread in 'New to the Hobby' later on to see if i can come up with any answers.