I am designing my radiant floor system on my two story with walkout home. My mechanical room is in the basement. My manifolds are at each of the levels in each zone. Do I need just one air eliminator in the master loop in the mechanical room or should I have one at each manifold location as well since these are the highest points in the system?

Hi,
You have the right idea, manifolds on each platform should have an air bleeder and hose bib for quick drain , boiler in mechanical room needs a air separator that will always be working.
We like to specify the B&G EASB-Jr Enhanced Air Separator, this is a good unit. you place it into the primary loop at a high point in the mechanical room.
Dan