In the samples installed with the SDK, they show how in DOInquiry.cs. It involves creating an invoice with that CustRef and passing it through.
// To use CUSTREF instead of PNREF you need to set the CustRef and include the INVOICE object in your
// request. Since you will be using CUSTREF instead of PNREF, PNREF will be "" (null).
// Create a new Invoice data object with the Amount, Billing Address etc. details.
Invoice Inv = new Invoice();
Inv.CustRef = "A54321";
InquiryTransaction Trans = new InquiryTransaction("", User, Connection, Inv, PayflowUtility.RequestId);