Hi Luke,
One way of dealing with the magnet between the rails as you have positioned them is to take a photo of a short length of ballasted track, print it out full size on a piece of good quality paper or thin card, cut out a length of the ballasted sleepers from your printed photo and then stick it down on top of the magnet. It won't look quite as good as fully ballasted track but it will look better than just the magnet.
I hope that helps,
Martin