I started using it from Orisson, about 8km after sjpp. Never used their website. There are special tags at the reception of every alberque/hostel. You just fill that up (name, destination, contact phone/email) attach it to the pack and leave it at the reception. Simple as that. At some alberques they would call the night before to confirm Jacotrans pick-up. So, do inquire at the alberques if that is necessary.
Several other pilgrims were emailing/texting them also. You will find all the details once you are on the Camino.