When creating an invoice, you can only reference an already existing entry in the company directory.
When adding a company to a new record in the directory, there are two options available:
Use the autocomplete feature available when entering the company name (type, for example, the first 3 letters of the company name, and Flexi will offer to load the company data from ARES).
Fill in the Company Registration Number (IČO) for the given record and use the Update from the internet button in the record header.