Finally I found an answer in com.avaje.ebeaninternal.server.deploy.DeployOrmXml#initialiseNativeQueries().
In case someone will stuck with this too I'll post an example:
orm.xml (in classpath):
<entity-mappings>
<named-native-query name="calculateCustomerTurnover">
<query>
select sum(total_usd) as turnover
from shipment
where partner=:partner_id
</query>
</named-native-query>
</entity-mappings>
in code:
SqlQuery query = db.createNamedSqlQuery("calculateCustomerTurnover");
query.setParameter("partner_id", customer.getId());
return query.findUnique().getBigDecimal("turnover");