You can configure the keystore in the properties file you configure using the attribute signaturePropertiesFile of the StaticSTSProperties class which is shared by all SAMLRealms. If you store several keys in one keystore, you can configure the signatureAlias in each SAMLRealm.
It's best practise to not share several private keys in a single java keystore. If you configure several realms in your STS deployment and each realm uses a different key to sign the saml assertion you must store all private keys in one java keystore.
Add the signaturePropertiesFile to the SAMLRealm too which is optional but if configured has higher priority than signaturePropertiesFile in StaticSTSProperties.