Which Java do you mean ?
Java used by BOE servers is SAP Java and cannot be manually upgraded, it is patched by regular product maintenance.
Java used when you run Java report panel to edit webi documents is client side, does not come with BOE and you can check it version in your control panel in Java control tool.
Java used by web application server is either the same as used by BOE servers if you are using tomcat provided with BOE (in this case you can install your own java and point that tomcat to use your version) or its java that came with your own web app server, in which case its upgrade is up to that webapp server vendor.