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The semantic segmentation of underwater imagery is an important step in the ecological analysis of coral habitats. To date, scientists produce fine-scale area annotations manually, an exceptionally time-consuming task that could be efficiently automatized by modern CNNs. This paper extends our previous work presented at the 3DUW’19 conference, outlining the workflow for the automated annotation of imagery from the first step of dataset preparation, to the last step of prediction reassembly. In particular, we propose an ecologically inspired strategy for an efficient dataset partition, an over-sampling methodology targeted on ortho-imagery, and a score fusion strategy. We also investigate the use of different loss functions in the optimization of a Deeplab V3+ model, to mitigate the class-imbalance problem and improve prediction accuracy on coral instance boundaries. The experimental results demonstrate the effectiveness of the ecologically inspired split in improving model performance, and quantify the advantages and limitations of the proposed over-sampling strategy. The extensive comparison of the loss functions gives numerous insights on the segmentation task; the Focal Tversky, typically used in the context of medical imaging (but not in remote sensing), results in the most convenient choice. By improving the accuracy of automated ortho image processing, the results presented here promise to meet the fundamental challenge of increasing the spatial and temporal scale of coral reef research, allowing researchers greater predictive ability to better manage coral reef resilience in the context of a changing environment.