The parts are made all over the world, as they are for almost all cars.
Major parts will be made in Spain, Germany, Czech Republic, Slovakia, Hungary and Portugal, depending on the car and the engine fitted. Sometimes identical parts will be manufactured in multiple locations.
Design engineering will mostly be shared between Germany and Spain, although the new Toledo's similarity to the new Skoda Rapid means Skoda's engineers in the Czech Republic will have had more involvement that with other Seat models.
Most models are assembled in Spain, although some are assembled at other VW Group plants (all Alhambra MPVs have been assembled in Portugal, all Mk1 Leons were assembled in Belgium, the Mii is assembled in Slovakia and the Toledo in the Czech Republic).
I'm afraid there is no straightforward answer, but it is the same for many cars.
My personal opinion is that those assembled in Spain are Spanish cars, but there is no clear-cut answer for the others, due to their similarity to models from VW and/or Skoda. They are simply European cars.
Is a Nissan Qashqai (styled, engineered and assembled in the UK, on a platform designed part in France and part in Japan, using a French-built diesel engine and a Japanese transmission, and badged by a Japanese brand) a British car, a Japanese car, or something else?