Most existing computational tools for assumption-based argumentation (ABA) focus on so-called flat frameworks, disregarding the more general case. In this paper, we study an instantiation-based approach for reasoning in possibly non-flat ABA. We make use of a semantics-preserving translation between ABA and bipolar argumentation frameworks (BAFs). By utilizing compilability theory, we establish that the constructed BAFs will in general be of exponential size. To keep the number of arguments and computational cost low, we present three ways of identifying redundant arguments. Moreover, we identify fragments of ABA which admit a poly-sized instantiation. We propose two algorithmic approaches for reasoning in non-flat ABA; the first utilizes the BAF instantiation while the second works directly without constructing arguments. An empirical evaluation shows that the former outperforms the latter on many instances, reflecting the lower complexity of BAF reasoning. This result is in contrast to flat ABA, where direct approaches dominate instantiation-based solvers.