To study a nuclear system in the Skyrme model one must first construct a space of low energy Skyrme configurations. However, there is no mathematical definition of this configuration space and there is not even consensus on its fundamental properties, such as its dimension. Here, we propose that the full instanton moduli space can be used to construct a consistent skyrmion configuration space, provided that the Skyrme model is coupled to a meson. Each instanton generates a unique skyrmion and we reinterpret the 8N instanton moduli as physical degrees of freedom in the Skyrme model. In this picture a single skyrmion has six zero modes and two non-zero modes: one controls the overall scale of the solution and one the relative size of the Skyrme and meson fields. We study the N = 1 and N = 2 systems in detail. Two interacting skyrmions can excite the meson field through scattering, suggesting that the meson and Skyrme fields are intrinsically linked. Our proposal is the first consistent manifold description of the two-skyrmion configuration space. The method can also be generalised to higher N and thus provides a general framework to study any skyrmion configuration space.