Two things to change around:
Drive the denitrator with water from the return side of the filter instead of using the intake. The reason is the filter uses up 02 in the nitrogen cycle. You want to start with the most O2 poor water that you can get.
Secondly, flip the in and out on the denitrator. If the water entering it starts at the bottom, then it will self purge.
This "was" exactly how I first had it. The reason its not like that any more was due to the internal pressure from the Fx5 due to the head pressure. I would have had to get this container level or higher than the water line for it not to leak.
I may be able to do it now that I have modified the seal for a tighter fit. All the reasons you stated are the reasons I had it connected to the output of the filter first.
The container does purge, but only when the Fx5 if OFF. The reason is due to the differential in pressures, as you already know. I did have it hooked up so that while the Fx5 was ON it would purge but this would allow air into the Fx5 which if you talk to any Fx5 owners, they get kinda loud when this happends.
To jump start the denitrator, empty it and clean some filters (sponges are best). Pour the dirty water in the denitrator, top it off and then just let it sit for a week or two. Give it a piece of shrimp or some fishfood to keep it going but don't open it to give it more food. At the end of the "cycle" period, it should smell really putrid. That is a good thing. Anaerobic activity doesn't smell nice. Aerobic activity has the cleaner smell, which is what you don't want. Contrary to what is passed around on the boards, a lot of bacteria can go from aerobic conditions to anaerobic and back to aerobic without missing a beat. This method of cycling will encourage the growth of those bacteria.
Thanks for the great tip. I will do just that

. So I should just, like you say, let it sit without any water moving in or out?
Before putting the denitrator back on the system, you are going to need to flush it with oxygen poor water from your canister. The denitrator will produce hydrogen sulfide during the cycle (it is very toxic to your fish).
I suppose I will fill a bucket up with water and let it sit for it to be depleted of oxygen.
I am also thinking that the very small amounts of hydrogen sulfide that are produced will get agitated out when it goes into the tank from the Fx5 since I have the output agitating the surface....?
You can get a better container from Walmart, many grocery stores, Kmart, Big Lots, etc. It is about the same size but round. They are made of hard plastic (looks like acrylic or polycarbonate). They have a silicone gasket and a metal latch for a tight seal. I'll see what I can do for a picture.
Maybe I missed it, but I didn't see anything better. Not saying there isn't, Target, Big Lots, Job Lots, may have something.