I am new to using SDSS image files and have noticed that some of the values in the FITS file are negative. Can somebody explain to me what these values actually mean?
Without more information about the specific nature of the fits file, my immediate guess is that you're using a file that has already been corrected for things like bias and flat fielding.
It is true that for a simple exposure (what we might call the "science" image), the fits image should have only positive values as each pixel is a (proxy) count of how many photons hit it and how can you have a negative number of photons hit your detector? But often astronomers need to clean up their science image from various sources of noise. One such example is cleaning it with a bias frame. A bias frame is an exposure with the shutter closed and the exposure time set to zero. Essentially you just pull the signal from the CCD without taking a picture. In a perfect world, the CCD will be blank and empty and there will be nothing to read out if you never exposed, but in the real world things are messy and you have lingering electrons all over the place. Reading a bias frame allows you to get some estimate of this noise that can inherently exist in a CCD. An astronomer will then take this bias frame and subtract it from the science image to remove this noise, but of course this can result in your science image having negative pixel values. This usually isn't a problem though.
This resource looks pretty comprehensive about the basics of cleaning science frames.
Without further details I would guess your fits file is using 16 bit signed integers between -32768 and +32767.
In which case you should find that the fits header item called bzero has been set to 32768.
The true integer values are given by your pixel value*bscale + bzero.
This is a very common format for raw data from CCD cameras.
On the other hand if you are talking about processed sky subtracted SDSS images, then of course some pixels are negative - the average pixel in a "sky" region will be zero, so a substantial fraction must be negative.