Here is one way of doing it:
Example:
90% base malt
7% specialty malt 1
3% specialty malt 2
1) Create a new recipe
2) Enter 90 lbs base malt
3) Enter 7 lbs specialty malt 1
4) Enter 3 lbs specialty malt 2
Off course your OG will be way off. To correct this, press the Gravity-button (or choose Actions -> Adjust Gravity), enter the desired target OG, press OK and BeerSmith will correct the amounts of grains to suit your needs.