As far as I know, there is no reason why you should not consolidate the thermostats into one unit. Nor can I think of a reason why you would have to have it on a particular floor. As you will see when shopping for the electronic thermostats, most of them are specifically designed to control the heat and the AC.
As far as which floor to put the dual-purpose thermostat on, I think this is a question of personal preference (where is it easier to get to? where do you spend more time in the house?).
If today your house is unevenly heated and/or cooled, you will want to account for temperature differences when setting the thermostat. For example, you do not want to set the heat for 68-degrees if the thermostat is on the first floor, but the upstairs bedrooms are 10-degrees warmer because of the heat rising.
The nice thing about the electronic units is that once you set them, you don't have to touch them very often!