Burp Suite Enterprise Edition will let you configure details of all your organization's web sites, so that they are available for scheduled scanning.
Sites can be organized into a tree structure using folders. You can use this to reflect the structure of your organization or infrastructure. You can also restrict user access to only parts of the sites tree, based on this structure:
Each site must be configured with the URL(s) at which it is accessed. You can also configure any sub-URLs which should be excluded, any application login credentials that should be used when scanning the site, and any default scan configurations that should be used: