I have not noticed UV filters to alter the photos you take besides giving you bad lens flares, ghosting, and reflections. I only use them to protect the lens. That's about it.
There are other filters that will change your photo, though, like circular polarizers and gradient filters.
The flash on the D90 itself should only be used for fill-flash when your subject is back-lit, creating a silhouette. The SB-600 will always be better than the on-camera flash, as it has greater power and range and can be tilted in such a way that will allow you to indirectly light up a subject by bouncing light from a wall or ceiling. With the D90 you can also control the SB-600 wirelessly with the pop-up flash. This allows you to pull off the flash from your camera and control the flash off-camera so you can position the light source differently.