I'll often leave the stringers proud of the formers a little or even scallop out the former between stringers. The reason being that if the stringers and formers are at the same height then the covering will adhere to both and make little rectangles all over the place.
That's really personal preference, but what you really want to avoid are stringers and/or formers of different heights or formers that stick out past the stringers. You'll often hear this look referred to as a "gaunt horse" because even after covered you can see the bones poking through everywhere.
Here is a scalloping example from my 500 series P-51. Click on a picture to see it close up.
http://www.virtualaerodrome.com/image_b ... &offset=24
Here is another of my kits that was not scalloped, but the stringers stick out past the formers pretty evenly everywhere. This was a laser cut kit so getting even stringer height everywhere was easy. Note the little rectangles formed by the formers and stringers.
http://www.virtualaerodrome.com/image_b ... &offset=12
I'll see if I can find a "gaunt horse" picture in such a way that doesn't embarrass the builder.