You can quote the value in the shell:

$ ./bin/config set notification.servers '{"key": "value", ...}'

Or you can read it from a file:

$ cat file.json
{
  "key": "value",
  ...
}
$ ./bin/config set notification.servers "`cat file.json`"

Or you can manually open phabricator/conf/local/local.json in an editor and edit that. bin/config is just a wrapper script which prevents mistakes and syntax errors.