Thank you for the advice. I will be working quite closely with any manufacturer in regards to the system. Right now it is looking like the ammonia chiller will operate the same as any chiller, but instead of R-410, ammonia will be used, as the building load is quite large, and there will be some desire for lower temps that R-410 just won't get. I'm not sure if the secondary medium will be a glycol/water solution or if a different type of medium will be required. Just how low the owner wants to go will determine this, and I don't know. I've done lots of research online, and with my ASHRAE books, and it looks like a lot of safety equipment will be required (eye wash, emergency showers, emergency push buttons, ammonia sensors, lots of airflow...), but the overall safety and maintenance will be on the owner. I am not going to design the ammonia chillers (thank god), but am tasked with finding a way to implement them into the building.
The responses above are great, and are being taken seriously, but right now determining the safety requirements is key. A saving grace also is that I don't believe that there will be enough ammonia in the chiller room to warrant meeting the EPA guidelines. This building should be well below the 10,000 lbs limit.