Best practice which I am using.
Write your code in a way so that you don't get StyleCop warnings from the very beginning of a project. The code you commit to your source control should contain 0 Errors (always!) and 0 Warnings (if there are warnings write a note in your changelog and/or
commit message describing why you committed code even it contains warnings)
Run the ExcludeStyleCop utility (e.g. see http://stylecop.codeplex.com/releases/view/48036) for a (large) legacy solution. If you touch/change a source code file remove it from the StyleCop exclusion and fix the StyleCop violations. Do a
commit with commit message ("code cleanup" or something similar). Then do the "real" coding changes. The two commits will help you to find the real code changes more easily (e.g. if you do code reviews). This approach will avoid that tons of code cleanups
are hiding real code changes.
Maybe you consider to use StyleCop via MSBuild. Maybe using FxCop too if you're developing class libraries.
--Harald-René Flasch (aka hfrmobile)