How VAT be setup for Trading in EU

Dear Tax Gurus,

We are trading company and is implementing VAT in Europe Union. And we have difficulties when source is out of EU / within EU, and customer is EU. For example, there are two scenario,  we buy product from non-EU and sell to EU customer, the input VAT and output VAT are both 0. However, if we buy from EU suppliers and sell to EU customer, the input VAT is 0 (if buy from branch company tax is 10%) and output VAT is 10%. We cannot determine the output VAT only by ship to. And the different source goods are stored