My understanding is that I can apply only one Mailbox Manager policy to a given set of users. Is there a way to work around this limitation?
The bad news is that you heard right. You can define as many Mailbox Manager policies as you like, but if more than one policy applies to a given mailbox (i.e., if multiple policies' filters include the mailbox), only the highest-precedence policy is applied. This limitation is compounded by the fact that you can apply only one action in a policy.
The good news is that there is a workaround. Say you want to implement a retention policy; to do so, you need to define two policies. The first policy is to move old mail from the Inbox to the Deleted Items folder after 60 days; the second policy is to delete mail from Deleted Items after 30 days, preventing people from filing old mail there forever. To accomplish your goal, you can schedule Mailbox Manager to run twice daily, then use a script to adjust the policy precedence so that the first policy runs during the first scheduled period and the second policy runs during the second period.