Good advice all
The reason you want to ask the bus driver "Directo a San Jose" is that some bus' stop first in Alaljuala - not the end of the world but you want directo.
Also - at the terminal, at the end of the ride - simply hail a taxi if you wish - going to the Hotel Morazon, with the taxi and bus fare, all in its less than $3 - with due respect to my friend RAC, unless you want to walk (I love to but not with a suitcase given the "sidewalks" in SJ

) and don't feel confident of directions, etc - take a taxi - you are still at least $10 ahead of the guys who took Interbus and >$20 to those who took a taxi from the airport.
More guys should consider the bus - its a great option (plus its easy and fast) and if you consider that you could save more than $20 - well, that savings bought you 2 lunches or a dinner - the other option I've used late at night is to share a cab - its ideal w/ 3 guys - and you don't all have to be going to the same hotel, just downtown.