By default, they are stored for each user under HKEY_CURRENT_USER\Software\VB and VBA Program Settings\CCleaner\Options except for the automatic update check which is a system-wide option (applies to all users) and is located under HKEY_LOCAL_MACHINE\SOFTWARE\CCleaner.
However, rather than plug the registry of your users, a better approach for "pushing" CCleaner, is to use the option for storing settings in an INI file. It would be named CCleaner.ini and placed in the same path as CCleaner.exe. And the easiest way to configure INI mode is to create a file named portable.dat in the same path, which forces CCleaner to operate in "portable" mode. Although portable mode is intended for use with USB flash drives, it doesn't do anything more than force CCleaner.exe to ignore the registry in favor of the INI file.
You can download the portable build of CCleaner by clicking on the "Other builds" link near the bottom of the download page, but there is absolutely no difference in the software between the builds; it's merely a packaging difference. The portable build is zipped (no installer) and comes with a pre-made portable.dat (which you could easily make yourself with Notepad).
