I'll try to explain with my own words...
"nondik" means "where from", in the sense of physical movement.
"nongoa" is also "where from", but in the more abstract sense of "stemming from"
Perhaps an example could help.
Kotxe hau Bilbotik dator = "This car comes from Bilbao", meaning that the car started its journey in Bilbao.
Kotxe hau Bilbokoa da = "This car is from Bilbao". In this case, you probably mean that the licence plate corresponds to Bilbao.
hope it helped... and otherwise, just ask again