I use the same house rule. It's pretty simple actually.
You do not consider the base attack and save bonus as integer, but as floating point numbers.
You've probably constated that simple formulae governs those values.
Good BAB = level
Medium BAB = 3/4 of level
Poor BAB = 1/2 of level
Good Save = 2 + 1/2 of level
Bad Save = 0 + 1/3 of level
You simply add up these fractional numbers together, but don't stack the possible +2 bonus of good save (the same way that in Star Wars d20, you don't stack the +2 Defense bonus of each class when multiclassing).
This way, each multiclassed characters will always have a BAB between 1/2 his level and his level, and saving throw bonus between one-third of his level and 2 + one-half of his level.
With standard rules, you usually get an unfairly low BAB value but sky-rocketing save bonuses.