To solve operator equations numerically, matrix representations are employing bases or more recently frames. For finding the numerical solution of operator equations a decomposition in subspaces is needed in many applications. To combine those two approaches, it is necessary to extend the known methods of matrix representation to the utilization of fusion frames. In this paper, we investigate this representation of operators on a Hilbert space with Bessel fusion sequences, fusion frames and fusion Riesz bases. Fusion frames can be considered as a frame-like family of subspaces. Taking the particular property of the duality of fusion frames into account, this allows us to define a matrix representation in a canonical as well as an alternate way, the later being more efficient and well behaved in respect to inversion. We will give the basic definitions and show some structural results, like that the functions assigning the alternate representation to an operator is an algebra homomorphism. We give formulas for pseudo-inverses and the inverses (if existing) of such matrix representations. We apply this idea to Schatten p-class operators. Consequently, we show that tensor products of fusion frames are fusion frames in the space of Hilbert-Schmidt operators. We will show how this can be used for the solution of operator equations and link our approach to the additive Schwarz algorithm. Consequently, we propose some methods for solving an operator equation by iterative methods on the subspaces. Moreover, we implement the alternate Schwarz algorithms employing our perspective and provide small proof-of-concept numerical experiments. Finally, we show the application of this concept to overlapped convolution and the non-standard wavelet representation of operators.