We have hundreds (or 1000s) of sites to build reports on, do I need to run one at a time?

No, the SharePoint Essentials Toolkit has an import option to import your list of Sites into the Home Page Dashboard. You can do this by clicking "Add Site->Import (from pop up dialog window)". The Home Page Dashboard supports thousands of Site Collections. You can group them to organize (right click the group name to rename them).

Once they are all imported, you can hold CTRL+Click to select the multiple sites, or hold SHIFT and select multiple sites to build a report on, then right click and select "Create Report". Once you select the type of report to run, a new window will open, the Site URL will be shown as "<Multiple Sites>", click "Schedule Job", and you can execute the job (in multiple threads) one-time or on a schedule. Once ready, click Save and the Scheduled Job for multiple sites will be appended to the "Scheduled Jobs" grid. You can access the Scheduled Jobs grid by clicking "Home (tab) ->Scheduled Jobs" to review them and their execution status. Right click them to view logs. Logs are also located in "Home (tab) -> Reports and Logs".

For more information, please see our documentation for the SharePoint Essentials Toolkit under "Batch Processing Reports for Multiple Sites", the documentation is included with the product download.