The navigation cell is a docked cell which is by default set when one chooses the SlideShow screen enviornment. This docked cell is specified in the notebook's style sheet. If one digs through the default style sheets to find this setting one finds that the docked cell is specified, not explicitly by a Cell expression but by the following:
FEPrivate`FrontEndResource["FEExpressions", "SlideshowToolbar"]
As far as I can see by looking through the Mathematica files in the application this must be an expression that is internal to Mathematica itself, rather than something that is read in from a file on startup.
If you open a notebook and simply execute the following you will see how this works:
SetOptions[EvaluationNotebook[],
DockedCells -> {FEPrivate`FrontEndResource["FEExpressions","SlideshowToolbar"]}]
As a result I don't see how to get access to the actual Cell expression that this generates for the DockedCell. If I could then I could pretty easily modify it and you could then create a special StyleSheet for your SlideShow which would have hting modified to your needs.
But.... failing that, you can use the SlideShow palette to generate a Table of Contents palette with the navigation buttons that you need and just position that ToC palette where you wish to on your screen.
Open the slide show.... then open the SlideShow palette.... then click on the Table of Contents button. This will create a palette with navigation tools for your slide show which you can plae where you wish.
