Deep space missions, and particularly cislunar endeavors, are becoming a major field of interest for the space industry, including for the astrodynamics research community. While near-Earth missions may be completely covered by perturbed Keplerian dynamics, deep space missions require a different modeling approach, where multi-body gravitational interactions play a major role. To this end, the Restricted Three-Body Problem stands out as an insightful first modeling strategy for early mission design purposes, retaining major dynamical transport structures while still being relatively simple. Dynamical Systems Theory and classical Hamiltonian Mechanics have proven themselves as remarkable tools to analyze deep-space missions within this context, with applications ranging from ballistic capture trajectory design to stationkeeping. In this work, based on this premise, a Hamiltonian derivation of the Restricted Three-Body Problem co-orbital dynamics between two spacecraft is introduced in detail. Thanks to the analytical and numerical models derived, connections between the relative and classical Keplerian and CR3BP problems are shown to exist, including first-order linear solutions and an inherited Hamiltonian normal form. The analytical linear and higher-order models derived allow the theoretical finding and unveiling of natural co-orbital phase space structures, including relative periodic and quasi-periodic orbital families, which are further exploited for general proximity operation applications. In particular, a novel reduced-order, optimal low-thrust stationkeeping controller is derived in the relative Floquet phase space, hybridizing the classical State Dependent Ricatti Equation (SDRE) with Koopman control techniques for efficient unstable manifold regulation. The proposed algorithm is demonstrated and validated within several end-to-end low-cost stationkeeping missions, and comparison against classical continuous stationkeeping algorithms presented in the literature is also addressed to reveal its enhanced performance. Finally, conclusions and open lines of research are discussed.