Named workspaces initially appear in the order they are declared in the config file.
When editing the config while niri is running, newly declared named workspaces will appear at the very top of a monitor.
If you delete some named workspace from the config, the workspace will become normal (unnamed), and if there are no windows on it, it will be removed (as any other normal workspace).
There's no way to give a name to an already existing workspace, but you can simply move windows that you want to a new, empty named workspace.
<sup>Since: next release</sup> Named workspaces no longer update/forget their original output when opening a new window on them (unnamed workspaces will keep doing that).
This means that named workspaces "stick" to their original output in more cases, reflecting their more permanent nature.
Explicitly moving a named workspace to a different monitor will still update its original output.