display another value

Not 100% sure I understand what you up to but here we go.
You can setup that second field as a dropdown as well and make it dependent on first dropdown box. In this case it will be filled automatically and you have an option to select different Link and Display fields.

Ok ill try make it clearer
jobs_add.php contains a field "customer"
the customer field uses a look up table to populate its self.
jobs_add.php also has a field "Quote No"
if your adding a job without having previously had a quote, the process is complete the form and save. When you select the customer form the look up table, the value it enters into the database is the customer unique reference. however the value it displays on the page is the customer name.
If however you have already a quote in the application you would use the look up table on the quote field. when you select your quote the auto fill completes the form. one of the fields the auto fill completes is the "customer " field. what happens then is the unique reference number is displayed and not the customer name.
I would like only to have the customer field display the customer name but save the customer unique reference number in the database.

I would suggest to make "customer" field a lookup wizard choosing "customer unique reference" as a link field and "customer name" as a display field.

This is how this field has been created. however it is also included in the auto fill process when the auto fill completes the field it shows the customer number and not the customer name

You can exclude it from Autofill list and make it a dependent dropdown box.

I would like to include it in the autofill selection

Autofill won't let you have different Link and Display fields. Dependent dropdown will and it works exactly the way you need it.