According to the documentation you should override the default configuration by placing properties files in tomcat/shared/classes/alfresco/extension/subsystems/Authentication and /Synchronization. To make Alfresco look there you should configure alfresco-global.properties by uncommenting the row about authentication and define your chain there (and the chain could have just one member, for instance ldap1:ldap).
At least that's how i interpret the documentation, however, I have not been able to get this working, so I think that either the documentation or the subsystems implementation is broken somehow.
The documentation says you should place your properties file in tomcat/shared/classes/alfresco/extension/subsystems/Authentication/ldap/ldap1 for instance, if you have a chain member named ldap1, but other threads in the forum indicates that the properties files needs to be placed in /Authentication/ldap rather than /Authentication/ldap/ldap1, which means that you could not have more than one chain member of a certain type (only one ldap for instance).
Sorry if this is all confusing you, but I'm pretty confused myself and I'm hoping that Mike F or anyone else might be able to sort this out.