Welcome to the KNIME Forum!
Let’s go to your questions:
- welcome page: what KNIME Server version are you using? Since KNIME Analytics Platform version 4.0, it is not possible to customize the Welcome Page.
- update sites: to customize update sides using your preference file add the argument /instance/com.knime.customizations/updateSite.uri= (to add the address of the update site) and the argument /instance/com.knime.customizations/updateSite.name=<name, e.g. Custom Update Site> (to provide a name for it) in the default.epf found in <server_repo>\workflow_repository\config\client-profiles\default.epf. Here you can find them how to set up in the client to request for Server profiles.
About your third topic: could you explain to me a little bit more what is unclear on the documentation? For many of these configurations, you can start your KNIME Analytics Platform, configure Python/R (for instance) or your Databases, export these preferences, copy them and paste them in the client-side epf, adjusting the paths accordingly. This is described in more details here (even more detailed description for how to deal with Databases can be found here).
In the folder <knime_server_repo>\workflow_repository\config\client-profiles.template you can find an example to get inspired.
Please let me know if it was helpful or you have any other questions