Which means "raskršće" in addition to name the place?


The bus does not go into the place (bus terminal), but stops on Highway.

What is "departure station"?


Departure station is the name of the town or city from which the journey begins.


What is "arrival station"?


Arrival station is the name of the town or city in which we wish to arrive.

What is the meaning of the "date" and the empty field, "day after"?


It will be shown time-table for a given date, and even as many days after the given date.
This option is usually used if we are not sure of the exact date of travel.

If allowed to be typing letters with special marks (š, đ, č, ć, and ž)?


Yes, has recommended their use. For some places has given a name and without these characters but certainly it is recommended use.

Terminology bus station, bus stop, ferry port


The term bus station is for one or more facilities where you can buy a ticket, wait for transport (waiting room), leave things for safekeeping and the like.
It is possible that there is only one service - ticket sales. In this case, the same station term is also used, which is most common in shipping when there is generally a ticket kiosk (aka ferry port).
A bus stop is a place where bus will just stop and there are no other services at that place. The rain and wind canopy is not the additional services.