1. A system for controlling performance of a selective catalytic reduction (SCR) system for reducing NOx levels in flue gas associated with a fossil fuel boiler having one or more generally cross-sectional areas, each cross-sectional area being characterized by a profile of a condition affecting SCR performance at said cross-sectional area, the system comprising: one or more devices associated with said one or more cross-sectional areas for adjusting the profile characterizing a cross-sectional area, said one or more devices operating in accordance with adjustable operating parameters; one or more sensors associated with said one or more cross-sectional areas for detecting conditions at said one or more cross-sectional areas; and a computer programmed to operate as an indirect controller for determining operating settings for the one or more devices, said indirect controller including: a system model that relates operating settings for the one or more devices to desired profiles of said conditions affecting SCR performance at said one or more generally cross-sectional areas, a controller input in communication with said one or more sensors, said indirect controller using the conditions detected by said one or more sensors, the system model, and the desired profiles to determine operating settings for the one or more devices, and a controller output in communication with said one or more devices to transmit said operating settings to said one or more devices associated with said one or more generally cross-sectional areas of the fossil fuel boiler; wherein said one or more devices include an SCR sootblower associated with at least one of said one or more cross-sectional areas for cleaning a surface in a catalyst bed to adjust a catalyst activity profile, an NH 3 injector associated with at least one of said one or more cross-sectional areas to inject NH 3 in said boiler and to adjust a NH 3 profile, and a fuel and air injector associated with at least one of said one or more cross-sectional areas to inject fuel and air in said boiler and adjust a NOx profile; wherein said one or more sensors associated with at least one of said one or more cross-sectional areas detect a NOx level, an NH 3 level, and catalyst activity at said one or more cross-sectional areas; wherein said indirect controller includes a system model that relates operating settings for the SCR sootblower to a desired catalyst activity profile, operating settings for the NH 3 injector to a desired NH 3 profile, and operating settings for the fuel and air injector to a desired NOx profile; wherein the indirect controller uses the NOx levels, the NH 3 levels and the catalyst activity detected by said one or more sensors, the system model, and the desired catalyst activity profile, the desired NH 3 profile, and the desired NOx profile to determine operating settings for the SCR sootblower, the NH 3 injector, and the fuel and air injector, respectively; and wherein the controller output of the indirect controller communicates with said SCR sootblower, NH 3 injector, and air and fuel injector to transmit said SCR sootblower operating settings to said SCR sootblower, said NH 3 injector operating settings to said NH 3 injectors, and said fuel and air operating settings to said fuel and air injectors.