Hi Scot,
Check Oracles site on how to, found this kbase article:
http://docs.oracle.com/cd/B19306_01/network.102/b14266/authmeth.htm
Found this for CR/BI/BOE:
http://anibalg.files.wordpress.com/2012/10/1748508-what-is-single-sign-on-sso.pdf
this should work but it's all Oracle and the Permissions issue, could be the type of connection you are using also, try ODBC or OLE DB. Possibly it has more features.
As for synonym's not showing up in CR it's always been that way. I believe it's the way or how Synonyms are defined by Oracle and what it's reported to CR by the Oracle Client. That always bugged me also....
I'll do some research on why and post it to Idea Place if it's something we can change.
Don