I only let the +2 count once for each saving throw and have AB and saves done fractionally. You can still "patch" a bad save with a 1-level dip but you don't get ridiculous cumulative bonuses from taking, say, four prestige classes with a good will save for example. Simply taking a prestige class shouldn't give you a free 10-20% advantage on saves compared to someone who goes straight base class, on top of all the other advantages from the prestige class.