In FME Server (2016.1) it is easy enough to manage named database connections. The capability exists on the "Manage Database Connections" page to create a new connection and edit an existing connection.
However, the same cannot be said for named web connections. The only current capability on the Web Connections page is to remove an existing connection. There is no support for editing existing connections or adding new connections.
This problem is compounded by the fact that there is no simple way to sync connections between FME Desktop and FME Server (See my other post: Easy upload of named connections from Desktop to Server).
I would like to see support for named web connections improved in FME Server.