Invoice reference (Your reference) and Our reference can be added to Company profiles and/or Individual profiles.
In Company profile they can be added to 'General' tab, at the lower part of the page.
In Individual profile they can be added to 'General' tab, at the lower part of the page.
If you create an Invoice for a reservation and there are values for either the Company profile references or the Individual profile references the references will be displayed below the invoice number on the invoice.
If there are values for both the Company profile references and the Individual profile references the value from Individual profile will be used. This is becasue different contacts at a company can have different references.
If you need to use a different reference then the one in the profiles you can click the 'Print settings' icon in Invoice view (cog wheel icon in top right corner). It will open a panel to the left where you can fill in other values for the references.