to be honest i don’t know zip about Shibboleth.
I’ d like to suggest these things :
You could start by looking for a php script / module / extension that talks with shibboleth ..
you might look at this wordpress plugin :
http://code.google.com/p/shibfaced/source/browse/wordpress/shibboleth.php?r=21
I once came accross a similar situation, but with an ldap ..; what i did:
users have a login name and password in ldap ..
i setup the same login names in modx (yes that is duplication)
then i wrote a plugin that would check the login and check the password they entered ...
this way the single logon and password would work
logon

present in ldap and modx manager user base)
password

present in ldap)
for the user the regular login password works ...
modx still generates its own password which also still works ...
this can come in handy from time ...
some things i learned (i was really a beginner at the time):
- apart from testing whether the Shibboleth (ldap) logon/password works .. you should check if a loginname and the wrong password resuls in access denied ! (initially my logon plugin worked ... for all passwords

- when migrating a production modx install .... disable this logon plugin first .. because (in mycase) the development environment cannot see/connect to the LDAP
this are I think the crucial code bits
$modx->Event->output($success); // this is what notices to modx whether logon was a succes
return;
where $succes is true or false