Hi Omar,

Assuming that your using the "Textbook" stylesheet that's found in the menu Format > Stylesheet > Book, and the Cell in question has the Cell style "EquationNumbered", you can add an autonumber for the "Section" to the equation number by modifying the CellFrameLabels for the style "EquationNumbered".

1. Select the notebook that you want to change
2. In the menus choose Format > Edit Stylesheet... This will embed a custom stylesheet into your notebook.

3. Paste the following Cell expression and click "Yes" when prompted "to interpret the text".

   Cell[StyleData["EquationNumbered"],
    CellFrameLabels->{{None, 
       Cell[
        TextData[{"(", 
          CounterBox["BookChapterNumber"], ".", 
          CounterBox["Section"], ".", 
          CounterBox["EquationNumbered"], ")"}]]}, {None, None}}]