Thanks, Aviatrix & Rambuster.

We received no instructions on visa application here and it seems weird if we stay here for only several months and we need to apply a visa to go back?

I'm already in Spain and when I asked the embassy of Spain which issued me the visa, they told me to take direct flight, which looks ridiculous as it's common that people buy return tickets...

I guess we only need the permit to enter EU (+1 transit) and we don't need that when we fly back? If they check my visa when I fly to Germany, they won't let me get on board as my visa is only national visa which doesnt allow me to other schengen states.