How Car Owner Points Are Awarded
Both car owner and driver points are awarded based on the same declining scale. The winner and his car owner each get 46 points plus one bonus point for leading a lap and one more bonus point for whoever lead the most laps.
Just like the drivers, car owners also see their points manually set to 2,000 with ten races remaining if they are in the top twelve plus three bonus points for each victory.
The driver point system is more thoroughly explained here.
How Each Are Used
The most important difference is how each of the point systems are used.
The driver points are used to determine the NASCAR Sprint Cup champion. This is what most people are talking about when they think if NASCAR points.
The car owner points are used in qualifying. Car owner points determine which drivers are locked into a guaranteed qualifying spot. They are also used to assign provisional starting spots. Finally, car owner points are used to set the starting lineup in case qualifying has to be canceled.

