Yeah,it can Very confusing.Sorry if I used the wrong phrase.
De-mineralization is NO3>>intermediates>>NH3
Ammonium is the main/prefered form of N in a seagrass bed.
Ah, I believe you're referring to "dissimilatory nitrate reduction to ammonium" (DNRA) process.
In terms of organisms, if you are mimicking the salinity of a lagoon ~25ppt, you could have tunicates(sea squirts) which are filter feeders and pretty awesome. Porcelain crabs are awesome and present in the lagoon, and while not native, they do thrive. In terms of corals & anemones and such, I haven't personally seen any, but I don't doubt they are in the IRL as it is very diverse.
The Smithsonian site lists a few corals/sea fans/anemones, but I am nowhere near knowledgeable enough to recognize names to get an idea of what would be available or what their requirements are...I'm assuming that they'd be found near some of the inlets.
I'm not quite so hung up on it being a strict biotope, especially if someone wants to convince me to go the coral/SW fish route

Seeing you're from Gainesville, have you had success purchasing from the LFS here? It's been hit-or-miss with the few FW things I've gotten...