[off topic]use webtemplates instead of sitedefinitions.[/off topic]

SPSite site = new SPSite("http://siteurl");
 SPWeb web = site.RootWeb;
 web.AllowUnsafeUpdates = true;
 SPLimitedWebPartManager webParts = web.GetLimitedWebPartManager("Shared Documents/NameOfMyPage.aspx", System.Web.UI.WebControls.WebParts.PersonalizationScope.Shared);

//Create an instance of Custom Webpart and add in a Webpart zone
 MyWebPart.MyPart wp = new MyWebPart();      // your custom webpart instance
 wp.Title = "My WebPart";   // set properties


webParts.AddWebPart(wp, "Left", 0);
 webParts.SaveChanges(wp);