Hello,
There is not a way to manually force the Auto-Clean rules to take place within SmarterMail. As for how and when these run, it is a scheduled thread that runs every 10 minutes.
One thing to note is that for an auto-clean task to be applied to a mailbox, a message does need to be received to that location. For example if you have an auto-clean rule setup for the 'inbox' of an account, no auto-clean rules will be applied to existing messages until a email is received to that folder.
Thanks