First introduced by Forman in 1998, discrete Morse theory has become a standard tool in topological combinatorics. The main idea of discrete Morse theory is to pair cells in a cellular complex in a manner that permits cancellation via elementary collapses, reducing the complex under consideration to a homotopy equivalent complex with fewer cells. In chapter 1, we introduce the relevant background for discrete Morse theory. In chapter 2, we define a discrete Morse matching for a family of independence complexes that generalize the matching complexes of suitable "small" grid graphs. Using this matching, we determine the dimensions of the chain spaces for the resulting Morse complexes and derive bounds on the location of non-trivial homology groups. Furthermore, we determine the Euler characteristic for these complexes and prove that several of their homology groups are non-zero. In chapter 3, we introduce the notion of a homomorphism complex for partially ordered sets, placing particular emphasis on maps between chain posets and the Boolean algebras. We extend the notion of folding from general graph homomorphism complexes to the poset case, and we define an iterative discrete Morse matching for these Boolean complexes. We provide formulas for enumerating the number of critical cells arising from this matching as well as for the Euler characteristic. We end with a conjecture on the optimality of our matching derived from connections to 3-equal manifolds