Your code is applying the trays to the selection rather than the document as a whole. Try this variation to make the trays independent of the selection when you run the macro.
Code:
Sub Section()
With ActiveDocument.PageSetup
.FirstPageTray = wdPrinterLowerBin
.OtherPagesTray = wdPrinterMiddleBin
End With
If ActiveDocument.Sections.Count > 9 Then
Application.PrintOut Range:=wdPrintRangeOfPages, Item:=wdPrintDocumentWithMarkup, Copies:=1, Pages:="S1-S10", _
PageType:=wdPrintAllPages, Collate:=True
Else
Application.PrintOut Range:=wdPrintAllDocument, Item:=wdPrintDocumentWithMarkup, Copies:=1, _
PageType:=wdPrintAllPages, Collate:=True
End If
End Sub