But how do you specify the data hyperparameter input and output models to use when the agent runs the experiment

They are autodetected if you are using Argparse / Hydra / python-fire / etc.
The first time you are running the code (either locally or with an agent), it will add the hyper parameter section for you.
That said you can also provide it as part of the clearml-task command with --args
(btw: clearml-task --help will list all the options, https://clear.ml/docs/latest/docs/apps/clearml_task#command-line-options )