Very much a question of personal taste.
I apply shading as part of the top coat application, ie paint the entire section in the base colour, then lighten specific areas, such as panel centres etc.
After applying the decals, and a coat of Furture, I apply a water colour sludge wash to the panel lines using a combination of black and burnt umber, varying the tone dependent upon the area of the airframe being weathered.
Once the sludge wash has been completed, and all unwanted wash removed, I apply a matt coat, followed by a light application of Tamiya Smoke along the panel lines. This helps tie the decals into the surface of the model.
I then apply a very dilute coat of Tamiya Dark Yellow, ie 9 parts thinner, 1 part paint over all the upper surfaces to tone down the overall weathering, and introduce a slightly faded, but not sun bleached look.
Here's an example;
Karl