In general, companies should register in the country from which their own goods are shipped. If a company ships goods from more than one country, it can choose a distribution location and register for the system there.
With the IOSS system, EU suppliers can either register in their member state or use an intermediary to do so. Registration is then done through the local IOSS authority. If they are from a non-EU country, they are required to register through an intermediary based in the EU. Now, once registered for IOSS, one gets a VAT number which is then valid for all transactions that fall under the IOSS rule.