Oh, found it. #### README.libmilter
Which filters are invoked and their sequencing is handled by the InputMailFilters option. Note: if InputMailFilters is not defined no filters will be used.
O InputMailFilters=filter1, filter2, filter3
Ah yes, the separator is a comma in confINPUT_MAIL_FILTERS in 8.12.x but it's a semicolon in the InputMailFilters= part of DAEMON_PORT_OPTIONS in 8.13.x. Watch out for this when you upgrade to FC3... if you use a comma you'll just be running the first of your milters and the rest will be ignored, something I fell over a few months ago.
Paul.