This is how I got to work. And you have to add the VCEngine reference with your project.
VCProject project;
Projects projCollection = sol1.Projects;
project = (VCProject)projCollection.Item(1).Object;
VCConfiguration config = project.Configurations.Item("Test Release|Win32");
IVCRulePropertyStorage rule = config.Rules.Item("ConfigurationDirectories") as IVCRulePropertyStorage;
//Setting the Include directories
string rawValue = rule.GetUnevaluatedPropertyValue("IncludePath");
string evaluatedValue = rule.GetEvaluatedPropertyValue("IncludePath");
rule.SetPropertyValue("IncludePath", "Whatever you like to specify here");
//Setting the Executable Directory
rawValue = rule.GetUnevaluatedPropertyValue("ExecutablePath");
rule.SetPropertyValue("ExecutablePath", "Whatever you like to specify here");