Remember, in summer the international trains tend to be full and you should book your seat at least a few weeks ahead. A few go to Praha Holesovice or to Praha Smichov or to Praha Masarykovo Nadrazi. All these stations have metro stops and are easy accessible. The best facilities has the Main Station. If you arrive in the middle of the night without a hotel reservation, store your bags and take a long walk inside until the sun rises.
Stations are magnet for pickpockets, crazies and at night it is a bad place.
Do not walk outside the stations. Also do not take a taxi from the Main Station. The drivers are involved in mafia and could be dangerous. Take a metro instead, it is safe in Prague. Bus Bus is the cheapest way to travel across Europe.