It looks like the fine folks at WotC have a clear understanding of what people find confusing about their ruleset. In what I must say is a far more exhaustive and clearminded article Does it Stack? they take the same look at bonuses and penalties that I took in Stacking – Types of Bonuses a year ago. They have released three installments so far, and if you don’t get the point by the end of part two, well… There’s more.