I normally just bump the base malt to get where I want to be, but I watch the percentages of the specialty malts to make sure they don't get too out of whack from the original recipe. Unless your efficiency is drastically different from the efficiency the recipe was written for, the percentages of the specialty malts won't change that much. Its an art, really. You have to use your beer-sense when adapting recipes to your system.
Primary/Secondary: #109 Rye, #110 APA
Kegged: #106 American Wheat, #107 IPA, #108 Nut Brown
Planned: Red IPA, American Brown