If you are dealing with a scalar navigation property, i.e. a navigation property that returns a single instance of another entity, then you can do it right in the createEntity call
newDetail = manager.createEntity("OrderDetail", { Order: parentOrder, Product: parentProduct });
If you are dealing with a nonscalar (i.e. array) navigation property then you will need to push the children into the navigation property. i.e.
newCustomer = em.createEntity("Customer");
var orders = newCustomer.getProperty("Orders");
orders.push(order1);
orders.push(order2);
// OR
// orders.push.apply(orders, ordersToPush);