Thermostat/blower placement for mini-duct A/C

I'm going to have a mini duct A/C system installed in my 4 level house on the top 2 levels (the other 2 stay cool because they're at least partly below ground and we live in MN). We have hot water heat with 3 zone thermostats. I'm thinking the thermostat should go in or near the master bedroom (all bedrooms are in the highest level) so I can control it easily at night (when I'll want to get up and turn it down). Any ideas about this? Because we have limited access to the two attics (24" square opening) the contractor wants to put the blower in an upstairs closet. Is this a bad idea?
Thanks in advance.
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