I have some land over there and hence visit a lot so heres what i do:
First of all, when you arrive, go to the customer information desks and ask to buy a bus and metro ticket. It should be 26 Czech Crowns (about a euro). Be careful and count your change as a lot of tourists are unfamiliar with the money and dont get the proper change. This ticket will be good for use on both bus and metro. It's an integrated system.
When you leave the airport, look around you should see a bus stop in front of you. There are several lines running so make sure you take the bus nr.119 that goes to DEJVICKA - its the last stop. It goes every 8 minutes so you won't have to wait long. Its roughly across the road and to the right as you exit the airport. There are airport officials who can advise you where it is if you get lost.
After getting off the bus you will see an entrance to the metro in front of you - station DEJVICKA, line A (green).
Take the train in the only possible direction (Depo Hostivar) as Dejvicka is the last station. If you get off at MUZEUM (the 5th stop) you will be fairly central and also able to transfer to the Red line if you follow the crowds. I think MUZEUM is really close to Wenceslas Square. Just find out which Metro stop is closest to where you want to be and then get off there.
This is exactly what I did in January so everything should be exactly the same and you should do fine if you follow these instructions exactly. This is the easiest way to do it. You cant miss the last stop for the bus and then you certainly cant miss the metro when you get off.
Ignore any taxi drivers who approach you at the bus stop. You have your 1 euro ticket and should be fine ;-)