Within sharepoint you can set permissions on a calendar basis, and on a per-item basis.
Essentially, there are 2 kinds of calendar items we have, both with different permissions. We'd like to simplify the permissions setting process, ideally so its automatic.
Is it possible to have the per-calendar-item permissions set automatically, based on (for example) a custom checkbox column?
Out of the box, no. BUT you can write an event handler, listening to ItemAdded event and ItemUpdated event which performs BreakRoleInheritance() and sets the required permissions. However, bear in mind that the results may be "interesting" if a user who added the item, does not have access to it after the event handler has performed its work (the user saw the item, then he/she refreshed the page and sees an error page).
What you are looking for is pretty much like SharePoint Permission workflow. However, I do not think it is applied to SharePoint Calender.