This question is not related to NWSSO. The correct space would have been SAP NetWeaver Portal.
Anyway, the answer to your question is that portal certificates have a subject which usually includes the SID of the AS JAVA. In STRUSTSSO2 you give access to a specific portal certificate and enable logon tickets by mapping the certificate to a SID and a client which in case of portals is always 000. In other words the SIDs of the 2 portals should be unique as well as the subject of the portal certificates which you upload to STRUSTSSO2.