The site is just new and needs a bit of tweaking (that will be done as the use grows).
If you are boarding the bus at Puenta Villa Bonita in Alajuela (near the airport), or at San Ramon, you still must choose San Jose as your departure point.
The bus driver has all the information on his smartphone and if you don't board the bus at the San Carlos station in San Jose, he will assume you will be boarding at Villa Bonita or San Ramon.
The ticket can be purchased as far as 3 months in advance.
The site is in Spanish and English:
If you have any problems, customer service at 2642-1112 is very helpful in Spanish and English.