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Using "Cover/Slip/Designate" function to print a booklet with a front/back cover printed on special paper and logo printed on back instead of inside.

Step-by-step guide

Ensure the document has a blank page before the last page, this is important if you are wanting the last page to have content otherwise it will print on the inside.
From the Printer Properties in the Detailed Settings tab select Cover/Slip/Designate from the Menu.
Set the following options:

Tick Front Cover Check Box
Select from Input Tray drop down: Select the tray you will be putting the special paper in as your Front/Back Cover. In this case Tray 3.
Select from Print Mode drop down: One Side
Tick Designate/Chapter Check Box

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Click Details... Button.
Set the following options:

Enter Page Number: Enter the number of the blank page just before the last page. In this case page 16 was the blank/second last page

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Select from Print Mode drop down: Designate: Both Sides
Select from Input Tray drop down: Select the tray you will be putting the special paper in as your Front/Back Cover. In this case Tray 3.

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As normal set any other desired options such as stapling.
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Info
It is important to note that the paper must be orientated in a specific way depending on the type of print job or the job will not print with no error message and papercut will still charge for the job.