Within the EU, the US and Canada (at least), you will find a great tolerance for this issue as many cultures order their names in different ways. The key is that the complete name, insofar as there are spaces, be listed. But, whether you list it as A,B,C,D or B,A,D,C will not be relevant.
I might suggest that you enter the information for APIS in the same order as it appears in the individual's passport. Even with the prickliest agent/border officer, you then have an official document which matches the information.