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To modify the sign on url for SAML, access the provided metadata url. Usually you would just paste this URL into the fdsso.config file. Instead, copy the xml contents and paste it into a file that is located on the FlexDeploy server (not inside the apache-tomcat-flexdeploy folder). Then modify the file as needed. Reference this new file path from the fdsso.config file instead of the URL.
Change from using the email address to another unique identifier with SAML
To modify the username that is used in FlexDeploy, change the Unique User Identifier (Name ID) claim in the SAML provider. No changes are needed in FlexDeploy.