Good question - one that I've thought about often myself.
I suppose there is some logical order to a series of filtration steps - although I don't think it's going to give a measurable difference.
I do think a prefilter sponge in the overflow is a must to reduce particles and suspended detritus from entering the wet/dry sump.
From that point on though - I see no huge difference in what order filtration occurs.
Typical scenerio - you have some amount of fish waste, ammonia/nitrite, CO2 gas, O2 gas and organic compounds that exist in your main tank saltwater. That saltwater passes through the sponge prefilter where much of the larger pieces of crud are removed, then the saltwater drains down to the sump area.
The saltwater moves through the protein skimmer and SOME of the organic waste is removed by the skimmer. Some of it yes - all of it - no way.
Then that same volume of saltwater moves through the wet/dry and biomedia where SOME of the ammonia/nitrite is converted to nitrate by bacteria. Again some of it converted - but not all of it. The saltwater is allowed to trickle over media and SOME gas exchange occurs. SOME CO2 is given off as gas, SOME O2 is consumed by bacteria, SOME O2 moves back into solution. But again - not all of it.
If you had a bag of activated carbon or polyfilter in the system down there, again SOME of the organic acids would be reduced by this pass over the chemical filtration media, but not all of them.
In a closed loop system, it's not like the waste in the water that enters the first stage, second stage, third stage and so on is COMPLETELY filtered on it's first pass. Some yes - all no. The saltwater recirculates around again for another pass, and another pass, and another pass and keeps going in this fashion, while all along, new wastes are being produced, gas exchange is occuring at the surface of the main tank, and the saltwater in the system is in a constant flux of being filtered and being fouled by contaminents.
If we had an open filtration system - like an RO/DI unit - where the water only gets one pass through each stage - then the order of stages is much more important. The water moves through each stage and it's a one shot deal - then out it goes.
Open system one pass only.
Closed system - many passes occur.
I'm sure others here would disagree with me, and feel that there is a logical order of what filtration should be done first, second and third ..... but to me, as long as the filtration method, be it biological or chemical, is in the system, it will do it's job - no matter where it is placed. I do feel strongly regarding the mechanical filtration being first though - as in a sponge prefilter - if you choose to use one.
So IMO - as long as the saltwater in your system is allowed to flow freely through each stage of your sump - and aside from the sponge prefilter being first - I don't see a need to redo your set up. Unless you just want a new protein skimmer
