the vortex generators (vgs) are like little dams placed at an angle to the flow. they force the air up and over them or around them, causing a swirl, like a little tornado. you can see this swirl start in a close up of flow over a simple angled plate shape:
the swirl pulls air above the surface - which has more velocity - down to the surface where the air has 'lost' velocity. this added velocity helps keep the air from separating off the surface.
you have to play with the size, shape, and location of these things. here's a shot showing my initial placement of some vgs on a wing:
without them, the 'bad' blue air separated right about where the little vortex generator is sticking up. it helped keep the flow attached a little longer. that is the blue area is father back, but the flow still separates.
the vgs on the top of the sidepods are probably trying to do the same thing - keep the flow attached to the sidepod upper surface instead of having it separate.
hope this helps explain a litlle better......
edit: i say 'probably,' because some of the little wing shapes on top of the sidepods may just be flow directors, not neceassarily vortex generators.