Issuing a Slovak VAT return from a Czech company with amounts in EUR is not possible,
however it is possible to obtain VAT data in the currency (EUR).
To do this, you need to have the Multiple VAT Registrations module enabled.
In the code list for the given country (Tools -> Code Lists -> Countries), you must have the VAT registration number entered. On the relevant documents, set the VAT Country to the Slovak Republic, select the appropriate Slovak VAT lines, and use EUR as the document currency.
The VAT return for a Czech company is always in CZK.