In most cases authentication via LDAP (including the Microsoft implementation that comes with "Active Directory") will be easiest and most useful:
/opt/shibboleth-idp/conf/ldap.properties to taste, according to section "Basic Configuration" from the documentation.
After changes to (any) property files you'll need to restart the whole container (i.e., Tomcat) for the changes to become active:
In order to test/verify your authentication configuration you may use the methodology described in our Testing an IDP documentation.
Further reading for more advanced needs:
Also, the ACOnet Team has collected working configuration examples from eduID.at community members, so you can always ask on the community mailing list or the provided support email address.