Hey guys, this are informations I got so far.
For small freelancers it would be best to register a specific kind of small business, like Goran sad, called "paušalni obrt". Because of unsure and unpredicted yearly income, when working as a freelancer, that should be most suitable considering taxes.
You will need some advice on how to register it, from some accountant, because that specific kind of business can't be registred for engineering professions.
Than write invoices to UpWork, which you never send to UpWork, but just for showing to tax administration. As far as I am informed, that's the way how companies in Croatia, that make money form iStore for example, justify their income. They write "dummy" invoices to apple because croatian tax administration still does not have suitable regulations for this kind of earning over internet.
I can't tell for sure if this process is valid because I haven't tried it my self. That's just direction towards wihch I got advices.