I have partitioned my hard drive so that the :C drive stores the OS, the D drive stores all programs, and :E stores my documents. How do I make CCleaner clean all partitions?
Welcome to the Piriform forums!
The first paragraph of this post gives some info about installing programs where CCleaner doesn't look due to how the cleaning routines are written. Although it's advised on some tweaking sites to configure Windows as you have done with Windows on C: and programs, etc., on another partition such as D: the unfortunate truth is CCleaner isn't going to be able to clean some or many applications on your computer.
The only option you'd have would be to modify the .ini files with the editable cleaning routines (for example; editable as those seen in the add-on winapp2.ini) in the CCleaner program folder.
Note: Not all of the cleaning routines can be modified, just those with specific directory locations can. This will of course be a very time consuming process for you to undertake, and you'll have to re-do it everytime you install a new version of CCleaner.