I've often wondered about this same sequence of different filtration stages, and I'm not yet convinced that it matters as much as many seem to think.
Reason being - I've yet to see any real numbers indicating what percentage of a particular waste is eliminated on a single pass past a particular piece of filtration equipment.
Is 100% of the ammonia converted to nitrite by the bacteria on bioballs, as a given volume of water during a given amount of time, trickles over them. I doubt it. Some if not most of the ammonia passed right on through this single pass.
90%
80%
50%
Who knows - I guess some percentage is removed, but it's a closed loop system. It's constantly removing or converting wastes upon each pass. Not a one shot nasty water in - good water out situation.
Same for a protein skimmer.
Same for carbon filtration.
Most of the wastes in the water passes through, only to be cycled over the media on an ongoing basis. At least this is my understanding.
Not the same for mechanical filter floss, prefilter sponges or pads. That IMO should always be first from the tank, to reduce small solid particles from entering the other following filter stages. Unless you are encouraging small plankton to recirculated in the system, and you are not using any mechanical filtraion. Then it's a moot point.
I suppose there is some logical sequence - meaning a little waste removed at stage one, then the water passes to stage two, and another form of waste is reduced a little more at that point, and so on and so on.
As long as the water passes through all stages unrestricted or without deadspots where waste can accumulate - personally I don't feel it matters all that much.
It's like trying to say where the best stage would be to place a submersible heater. It doesn't really matter ( unless you lose your return pump water flow ).
Others I'm sure will disagree with this - and that's cool.
I don't mind a good discussion - and would like to hear what others think, but please back it up with solid facts - or else it's just speculation and opinion, and I've already mentioned mine here