Most recent versions of SmarterStats remove spider/bot activity automatically and put those numbers in their own reports. You don't need to manually filter anymore. As for the difference in the numbers you see between GA and SmarterStats, we explain some of that in our help document for Stats: http://help.smartertools.com/SmarterStats/v11/Topics/Concepts/GoogleAnalyticsComparison.aspx
Derek Curtis
COO
SmarterTools Inc.
www.smartertools.com