Background: Closing on a custom built home at the end of August.
House Facts:
Total Sq Ft = 3400 (1st Flr is about %60 and the 2nd flr is about %40)
Air System: (2) Amana 14 Seer; 1 for the 1st flr & 1 for the 2nd flr.

Each floor will have it's own Air/heat and it's own thermostat.

My questions is what is typically the best place to put the thermostat?

I always thought you were suppose to center it, as best as possible, in the house to ensure as consistent a temp as possible throughout the house. My builder has for some reason not done this. While checking out the house this past weekend I found that the 1st floor thermostat is about 20 feet from the front door, on the wal that is in the main/front entranceway to the house. This open area of the house has no second floor and it's where the open formal dinning area and study are. The Master BdRm & Bath are twice the distance from the thermostat then the front door is.

The second floor thermostat is in an even worse spot. It's inside the middle bedroom on the back side of the house. This makes no sense to me. It's not as far from the center of the upstairs as the thermostat on the 1st floor but it's inside one of my little girls bedroom. AT some point she's going to want to close her bdrm on occasion. How in the heck can a thermostat regulate the air correctly in that kind of setup?

I'm insisting that the builder move the thermostats or provide in writing a guarantee that the average temp throughout the hsoue will not deviate by more then 2 degress from the thermostat else come out and make the system work and if they can't then move them or pay the extra cost it will take to cool/heat the outer areas of the house.