speedlight question with Nikon

I'm just received a adorama twin blitz speedlight with a Nikon D80 camera. When put in M, A, or S the flash is just fine, still experimenting with settings (open to tips). But for general use, I put it on auto, when I do the pop-up flash on the camera tries to pop up, it only gets 1/2 way due to the speedlight being in the way, and it does not flash. I was wondering if this was bad for my camera, and if the camera is reading the speedlight in auto, are there settings for using a speedlight (the manual isn't much help...)?

Thank-you

The on-board flash opens up because the camera doesn't know there is a flash in the hotshoe. Since the flash you have isn't a "dedicated" flash, the camera doesn't communicate with it other than to trigger the center pin to fire it. I've used manual non-dedicated flashes for years. You just have to learn how to use it and it should serve you well.