Deploying the IFS Applications Middle Tier using the IFS Applications Installer involves creating an <ifs_home>, building the Application Server packages and deploy those packages. Clients are deployed to servers for user assisted deployment (Click-Once for IFS Enterprise Explorer).
When running an upgrade, you should always start with a new <ifs_home>. It could be wise to backup your old <ifs_home> first, this has to be done manually.
This means in practice that an upgrade of IFS Applications Middle Tier is identical to a fresh installation. Link below about how to deploy are therefore pointing at the Fresh Install Guide.
Please also note that if your current IFS Applications Middle Tier installation is clustered and using Single Sign-On this must be reconfigured in your "new" installation.
If upgrading from JBoss installation to IFS Middleware Server make sure that you have bought sales part IFS Middleware Server and have the component in your build. Also note that IFS Middleware Server is clustered as default and is very easy to expand with more nodes.