You need to make the track grade wider than what is really needed at the point where the bridge goes over the tracks. Once you've got this, you then need to use the smallest radius tool possible and raise the ground up under the bridge foundation. I will measure the height of the bridge, and then use the same height in the topology height setting to make sure the ground comes up under the bridge. I then make final minor adjustments afterwards using the up-down adjustment so that the bridge doesn't looke like it's floating over the tracks.
I hope this helps. It's easier to do than explain!
John