I have been looking at a electrical blurprint for a heating and air conditioning unit. Power coming in the transformer is 120v and neutral. On the secondary side is power going out (24V) hot on each wire in which there is only two?

What are you wanting to do? The secondary will have 28 volts between the two wires. A common and a hot.

I am trying to read an old blue print about 25 years old as much as the ac and heating units. The secondary side shows voltage going to the thermostat and to the other circuitry.
I needed to know if the theromstat is energized at the same time as the relays.

Yes the red wire to the t-stat should get power as soon as the unit is turned on.