Colloidal suspensions consisting of solid particles in a fluid are ubiquitous in industry and everyday life. The flow properties of these materials are governed not just by the properties of the individual solvent and the particles, but also by the microstructure formed under flow. In this thesis, we show how we can understand and tune the flow properties of colloidal suspensions by studying and altering the microstructure, both at large flow rates and under confinement. At high flow rates, dense suspensions undergo shear thickening or an increase in viscosity with increasing stress. The microstructural change driving this increase is the formation of frictional force chains between the particles in these systems. Here we show that the viscosity of shear thickening suspensions can be decreased and tuned by applying orthogonal shear flows and acoustic perturbations that disrupt these force chains. By carefully tuning the duration of the perturbations and the applied flows we can generate viscosity metamaterials, which display different viscosities when probed at different time scales. As these protocols rely on altering the microstructure, it is important to understand the spatial distribution of the force network in shear thickening suspensions. We demonstrate a new technique, where we measure the instantaneous stress response after changing the direction of shear to determine the angular stress distribution. These multidirectional flows used to probe and manipulate the suspension leads us to develop a universal scaling framework that not only captures steady state shear thickening but also orthogonal superimposed perturbations and can easily be extended to other shear flows. Moreover, the scaling framework elucidates the close connection between shear thickening and critical phenomena, opening the door to importing the vast knowledge of equilibrium statistical mechanics into shear thickening. Finally, we focus on suspensions under confinement, where the presence of boundaries leads to numerous different microstructures. We study the role played by these structures in altering the forces between the particles and the resultant suspension viscosity both at low and high shear rates. Together, these studies elucidate the role of the microscale particle arrangements on the suspension viscosity and will be important for future work ranging from studying the statistical physics of shear thickening and yielding in amorphous materials to engineering fluids with specific flow properties.