Beersmith does have a 'scaling' option. In fact i am using it today to scale a usual 5gal recipe to a 3 gallon recipe. Just highlight your recipe, then click the scale icon in the toolbar above and a window will pop open and you can plug in your new batch size and BS takes care of the rest.
You could save the 2+ gallons and add as exaporation occurs. I don't suppose it would much different than adding extract.
If your game, you could reduce the extra 2.25 gallons in another pot down to say 1 gallons and then add it back to the main boil. This is a technique used in Traquair House ale (I'm sure others), to get more depth of flavor. But, your beer will obviously change.