By default, going to Appearance -> Widgets will present widget areas (sidebars) of all the layouts present in your iThemes Builder site. Having a long list of widget areas will make it cumbersome to drag widgets into widget areas when you are looking to populate widget areas of a specific layout.
Builder makes it super easy to reach to widget areas of a particular layout in two methods.
Visit any page in the site that uses the layout whose widget areas you want to populate. Ensure that WordPress Toolbar is visible (can be controlled by going to your profile page). Hover on Builder in the Toolbar and click Manage Widgets for this Layout.
In the WP dashboard go to layout manager at My Theme -> Layouts & Views. Hover on a layout and click Widgets link.