Each track or track-group creates a JACK midi output. You can use any jack patch tool, like catia, carla, qjackctl or the pipewire tools to connect that to your sampler(-hardware)
See here: https://youtu.be/1e3bQTpvbqk?t=86
There is no MIDI input except the APC controller, which was just a test. But you mentioned you want a clock. Patroneo works with the JACK transport system, which makes it play at whatever tempo your system provides. There are ways to use an external clock as jack tranport time, but I can't explain that here (because it is outside of Patroneo).
See here: https://youtu.be/Cu963-3rqVA?t=7