The toolkit was designed for Site Owners, Site Collection Administrators and Farm Admins. So sometimes a Site Owner may only have access to certain sites but not the web application, therefore the tool does not try to enumerate all of the site collections and sites in a web application automatically.
To add all of the site collections from a web application automatically, you can use the Add Site->Import option
You need to have a MS Excel spreadsheet with a list of all of the Site Collections, you can use PowerShell below to get these and you only need to import once to get them listed.
get-spsite -limit all -WebApplication http://contoso | Select Url | Export-CSV "C:\Users\yourusername\Documents\spsites.csv"
Adding new subsites will not change the report data, they can be added any time after into the tool.