Yes, you are right on Querybuilder link.
http://MyServer:Port/AdminTools
2. You can give like
SELECT * FROM CI_INFOOBJECTS
WHERE SI_PARENTID= (ID of the company name1 folder). This will pick up all the folders and reports under that parent ID. If anyone add the reports, in the next run, it will pick up all the new ones.
Assuming that your folder structure like this Company Name1
Dept Name1
Folder1
Folder2
Dept Name2
Folder1
Folder2
Setup the scripts to run when the BO system is not in use. Like Midnight. How often you are planning to setup to run the scripts? Daily, Weekly or Monthly?