Quantum computers may solve some computing tasks more efficiently than classical com- puters, but to do so requires the design of appropriate quantum circuits. However, it is hard to design even simple quantum programs. Recent results have shown that deep learning augmented search has the potential to discover good circuits for a problem, but it is not yet sufficiently understood how well deep learning is able to model such a complex domain: the search space and output space grow exponentially. This work explores the ability of neural networks to encode quantum circuits for tasks that require knowledge about the unitary representation of the circuit. To this end, we trained neural networks to directly learn to predict the unitary of a circuit and applied reinforcement learning to train neural networks to solve circuit based quantum state preparation. This work finds that encoding quantum circuits is quite difficult especially with regards to the amount of entanglement applied in both application domains. The use of intermediate states and structure in quantum circuits combined with a reasonable inductive bias, where applicable, can alleviate these problems to some extent. The use of intermediate states also greatly improves the results of Deep Reinforcement Learning for quantum state preparation. Based on these results, we discuss the next set of challenges to address if we are to design neural network-based approaches for the automatic generation of quantum circuits.