1. A computer-implemented method for configuring application control rules, comprising: generating a new application control rule that specifies restrictions or a permission on executing a software application, a function of an application or a category of applications; collecting information about one or more computers in a network, the information comprising information about software applications deployed on the one or more computers and one or more existing application control rules associated with the software applications; determining a priority for each of the new application control rule and the one or more existing application control rules; testing, by a processor, the new application control rule using the collected information to determine verdicts rendered by the new application control rule that restrict or permit an execution of the software application, the function of an application or the category of applications; comparing verdicts rendered by the new application rule with the verdicts rendered by the existing application control rules to identify conflicts between the compared rules; and upon detecting a conflict between the compared rules, reconfiguring one of the compared rules with a lower priority to eliminate the conflict.