Most of the rule types (priority, affinity, etc..) allow you to order the rule list in the 'Options' menu config dialogs. This sets the precedence for rules of the same type. When a process matches a rule, further rules of the same type aren't evaluated for that process until a rule configuration change occurs.
For cases where an algorithm or rule come into conflict, for instance CPU Limiter and CPU Affinities, the algorithm takes precedence.