This is all in bullet points at the bottom for anyone who has a grasp of tank and filter dynamics etc is short on time or who just couldn't be bothered reading the detailed answer.
Once it's fully cycled and the new filter is home to it's full compliment of bacteria I won't be at all concerned really. Right now were into the disgusting brown algal bloom watch the ammonia closely stage of the cycle - YUCK!
There are a few reasons why I'm not worried about it.
Mostly it's is because the tank and more specifically the filter will never be pushed to it's maximum capacity/capability. It's called the bioload and there is ample filtration and surface area within the canister filter alone to cope with the ammonia produced by 9 -10 axies a few guppies and a colony of cherry shrimp and their poop/food scraps even without spot cleaning and then I have the added bacteria laden bioballs within the hill that will also add to the capabilities of the tank to complete the nitrogen cycle. It now has a 2000L/hour filter on it and because it's all pumped down into the hill I have almost no water disturbance to stress the axies. The tanks construction makes such a large filter possible. I don't think I could run it in the conventional way with a spray bar straight into the tank it would simply cause too much flow for an axie.
What it all boils down to is this. In a fully cycled tank with adequate filtration you should never really see ammonia or nitrite unless there is some sort of catastrophe like your 3 year old dumping a whole canister of fish food flake into the tank

or an animal dying and going undiscovered for a short time OR the rapid addition of more animals. This last one obviously is only an issue for the short time it takes for the bacteria to increase in numbers again to cope with the new load but it is worth being aware of.
If your tank fully is cycled and you still get ammonia then you need a bigger filter as the one you have is simply not big enough, it lacks sufficient internal surface area to host the bacteria needed to cope with the tanks bioload. You'd need to find a way to increase it's filtration power, reduce the bioload OR get a bigger filter.
So if you don't get ammonia and Nitrite in the tank your only real problem is Nitrate which is readily used by the plants. The more plants you have the more of the Nitrate they will use and this tank will have a LOT of plants when it's all finished growing.
Now all that said the sand is still going to get dirty and it will still need cleaning which will mean fairly regular water changes which will also help to keep Nitrate well under control.
That is also a whole lot of water for the odd missed axie poop to pollute so the sheer size of the tank will also play an important role but the shrimp and guppies in the tank will show signs of a problem before the levels are high enough to hurt the axies giving me valuable time to locate the problem and take appropriate action to rectify it.
Last but not least I have a brand new master test kit I bought today that needs to be opened and used by the end of 2014 and I plan to get my monies worth out of it so will test regularly.
And as promised for those who couldn't be bothered reading all that 
* More than adequate biological filtration once fully cycled
* Huge numbers of live plants
* Regular cleaning and resulting water changes
* Large water volume to buffer against any missed ammonia sources.
* Weekly to fortnightly water testing
* The early warning ammonia/nitrite detection system. ie. the guppies, Cherry shrimp and glass shrimp in the tank will show signs of water problems well before they reach levels that would affect the axies. :happy: