A reference list can be included in the same metadata deposit as the bibliographic metadata for a given publication, or they can be submitted in a later, reference-only deposit.
This is an example xml metadata deposit for an article with references included:
And this is an example xml resource deposit, adding a reference list to the metadata a previously-registered DOI:
For the first, you’d use the operation doMDUpload in a https post command.
For the second, you’d use the operation doDOICitUpload.
I hope that helps clarify things for you. Let me know if you have any additional questions.