Second-order conformal quantum superintegrable systems in two dimensions are Laplace equations on a manifold with an added scalar potential and three independent 2nd order conformal symmetry operators. They encode all the information about 2D Helmholtz or time-independent Schrödinger superintegrable systems in an efficient manner: each of these systems admits a quadratic symmetry algebra (not usually a Lie algebra) and is multiseparable. We study the separation equations for the systems as a family rather than separate cases. We show that the separation equations comprise all of the various types of hypergeometric and Heun equations in full generality. In particular, they yield all of the 1D Schrödinger exactly solvable (ES) and quasi-exactly solvable (QES) systems related to the Heun operator. We focus on complex constant curvature spaces and show explicitly that there are eight pairs of Laplace separation types and these types account for all separable coordinates on the 20 flat space and 9 2-sphere Helmholtz superintegrable systems, including those for the constant potential case. The different systems are related by Stäckel transforms, by the symmetry algebras and by Böcher contractions of the conformal algebra so(4, C) to itself, which enables all systems to be derived from a single one: the generic potential on the complex 2-sphere. This approach facilitates a unified view of special function theory, incorporating hypergeometric and Heun functions in full generality.