In this paper, we propose a ground-based monocular UAV localisation system that detects and localises an LED marker attached to the underside of a UAV. Our system removes the need for extensive infrastructure and calibration unlike existing technologies such as UWB, radio frequency and multi-camera systems often used for localisation in GPS-denied environment. To improve deployablity for real-world applications without the need to collect extensive real dataset, we train a CNN on synthetic binary images as opposed to using real images in existing monocular UAV localisation methods, and factor in the camera's zoom to allow tracking of UAVs flying at further distances. We propose NoisyCutout algorithm for augmenting synthetic binary images to simulate binary images processed from real images and show that it improves localisation accuracy as compared to using existing salt-and-pepper and Cutout augmentation methods. We also leverage uncertainty propagation to modify the CNN's loss function and show that this also improves localisation accuracy. Real-world experiments are conducted to evaluate our methods and we achieve an overall 3D RMSE of approximately 0.41m.