Create a sitecore Item with WFFM form as a source and assign presentation to it in code.

           
              Database database = Sitecore.Configuration.Factory.GetDatabase("master");
               Item item =  //Sitecore item to which wfm form will be assigned
               Item wfmItem =  //wfm form item which to be assign         

               Item formLayout = database.GetItem("{6D3B4E7D-FEF8-4110-804A-B56605688830}");                   // Rendering used Form/Mvc Form , here i am using Form
                //Renderings/Modules/Web Forms for Marketers/Form

                string renderingXml = item["__Renderings"];
             
                LayoutDefinition layoutDefinition = LayoutDefinition.Parse(renderingXml);
         
                string defaultDeviceId = "{FE5D7FDF-89C0-4D99-9AA3-B5FBD009C9F3}";

               // Layout/Devices/Default item id

                DeviceDefinition deviceDefinition = layoutDefinition.GetDevice(defaultDeviceId);

                string sampleRenderingId = formLayout.ID.ToString();
             
                RenderingDefinition renderingDefinition = new RenderingDefinition();

                renderingDefinition.ItemID = sampleRenderingId;
                renderingDefinition.Datasource = wfmItem.ID.ToString();
                renderingDefinition.Placeholder = "main"; // ContentPlaceHolderName;
                deviceDefinition.AddRendering(renderingDefinition);
                string outputXml = layoutDefinition.ToXml();
                item.Editing.BeginEdit();
                item["__Renderings"] = outputXml;
                item.Editing.EndEdit();

                // The publishOptions determine the source and target database,
                // the publish mode and language, and the publish date
                  PublishOptions publishOptions =
                  new PublishOptions(item.Database,
                                                         Database.GetDatabase("web"),
                                                         PublishMode.SingleItem,
                                                         item.Language,
                                                         System.DateTime.Now);  // Create a publisher with the publishoptions
                Publisher publisher = new Publisher(publishOptions);

                // Choose where to publish from
                publisher.Options.RootItem = item;

                // Publish children as well?
                publisher.Options.Deep = true;

                // Do the publish!
                publisher.Publish();