The two 24 volt wire that runs from the condenser to the mother board of a goodman heating unit go on what terminal?

The goodman unit has a wiring diagram on the inside of the blower door on the inside unit/furnace.. It will tell you there.

Generally one is connected to common the other to y terminal

ccc0427 is exactly right.
Also it makes no difference wich wire goes y and c
You must also make sure that you have correct wiring from the thermostat. Please give more details as to what your setup is.