We bought the tickets ahead of time via the internet. The ticket lists the station, the time of your departure and the number of the bus docking station where you will board your bus.
The numbered docking stations.
We arrived about 30 minutes ahead of time and waited patiently at the correct number for our bus. The time came and left and the bus didn't come. I confirmed with the other people waiting if they were also waiting for the bus to our stop over in San Sebastian. They said they were indeed. I was clearly in the right place.
After a long wait, everyone became confused and started to go up to other buses headed to San Sebastian. When we asked the bus drivers if they knew where to find our bus, they said they didn't know. Eventually we somehow got on some other random bus headed to our stop over.
By time we got to our stop over, our connecting bus had already took off almost one hour ago!!! We waited until the next bus heading to our destination hoping to get on, like we did in Pamplona but alas he said our name was not on the list.
To add further confusion to this mayhem, your ticket may say that your bus will be the company ALSA, but the bus at your dock will be with CONDA and have a small ALSA sign. Sometimes that sign might even be printed out on the computer!!! Easy to miss.
He sent me to the ticket counter down the road with our two big suitcases. We waited in the long line. I knew some Spanish, but couldnt communicate well with the the woman behind the glass as I couldn't hear her clearly. She became angry with me and called me crazy. Eventually she came from behind the glass and explained to me I can wait until tomorrow, because there are no buses left for today.
Because I already paid in full for my hotel in the next town, I sucked it up and ended up paying $200 for a taxi, and I never got a refund on my second ticket for the bus I missed.
Unfortunately I can't recommend anything to avoid this whole fiasco. All you can do is hope for the best.
Our bus ride back on the way back had no hitches. It arrived on time at the correct dock.