The Maunakea Spectroscopic Explorer (MSE) project is an enterprise to upgrade the existing Canada-France- Hawaii observatory into a spectroscopic facility based on a 10 meter-class telescope. As such, the project relies on engineering requirements not limited only to its instruments (the low, medium and high resolution spectrographs) but for the whole observatory. The science requirements, the operations concept, the project management and the applicable regulations are the basis from which these requirements are initially derived, yet they do not form hierarchies as each may serve several purposes, that is, pertain to several budgets. Completeness and consistency are hence the main systems engineering challenges for such a large project as MSE. Special attention is devoted to ensuring the traceability of requirements via parametric models, derivation documents, simulations, and finally maintaining KAOS diagrams and a database under IBM Rational DOORS linking them together. This paper will present the architecture of the main budgets under development and the associated processes, expand to highlight those that are interrelated and how the system, as a whole, is then optimized by modelling and analysis of the pertinent system parameters.