The 47.66mhz system goes through EMRC first. There is actually no EMS radio equipment located physically at any hospital itself. All of the RF goes through the EMRC system and is patched to the hospital's remote set via hardline or microwave. This allows ensured communication between an aircraft (or ground unit on UHF) and a hospital that may not be within RF range, and allows multiple hospitals to be brought together in a single consult. The heli-med 47.66mhz system has only 7 base stations state-wide.
As far as using 47.66mhz versus UHF med, I'm really not sure how that decision is made. Perhaps there is just a general knowledge among the flight crews and the SYSCOM/EMRC operators as to where one works better than another. Of course, the UHF med system is designed for land mobile coverage (down-tilts, voting thresholds), and a helicopter could quickly move through and out of the coverage of a certain region's med channels/PL tones. I'll ask around and see what I find out.
Add: the flight crew do have access to UHF portable radios with the med channels if they need to obtain medical direction while on scene and out of the aircraft as well. Although, I've never seen one actually being carried.