In order to have different printer settings for different parts, you need different sheets. (As Excel doesn't allow to have different pages in the same sheet with different printer settings).
Then you can print all the sheets in the same long document by selecting to "print all sheets" (In the Custom preview demo, look at the "All sheets" checkbox at the left)
Now, this would apply to printer settings like landscape/portrait or different page sizes. I don't think it will apply to printing duplex or not, because this isn't an Excel setting but a printer setting (and not all printers support duplex printing).
To change this in a page by page basis you might need to use the BeforeNewPage event of FlexCelPrintDocument and change the Duplex setting of the printer depending on the page.