BeerSmith accumulates all sugar sources in the OG total, regardless of when the sugar addition takes place. This drives the Brewhouse Efficiency and abv numbers. BeerSmith doesn't model the use of multiple yeasts, either. It simply takes the broader view that all sugar is eventually consumed, leaving the brewer to do the job of making notes on the infinitely complex variations of late sugar additions and refermentation.
Brad has said that there need to be changes to how BeerSmith handles sugar additions. He hasn't said how these changes might work or when they'd be updated.