Gelfand-Tsetlin polytopes are prominent objects in algebraic combinatorics. The number of integer points of the Gelfand-Tsetlin polytope $\mathrm{GT}(λ)$ is equal to the dimension of the corresponding irreducible representation of $GL(n)$. It is well-known that the Gelfand-Tsetlin polytope is a marked order polytope; the authors have recently shown it to be a flow polytope. In this paper, we draw corollaries from this result and establish a general theory connecting marked order polytopes and flow polytopes.