The most important source for everyone who is researching Czech ancestry are the registries (parish books). Every village was a part of a parish since the middle ages and every parish is stored in some archives, so first of all you need to know to which parish (and archives) the village of your ancestors belonged to.
How to determine it? The best site I've ever found is Mr. Gundacker's GenTeam.at. It's available in English and the most important part of all is the Gazeteer. You'll have to create an account to access the information on the website, but believe me, it's worth it. When you get the login information and you are signed in, you'll see Gazeteer in the left menu:
You can search for the location in the main "window" after clicking on Gazeteer in menu. You can put there only a part of the village name so if you are not sure about the spelling, you will see more possibilities in the search results. I've searched for village Chlistovice (thanks, Coodi!) and put there only "chlistovic". Here is the result - you can see former village name, current village name, parish under which the village belonged, and crown land it was in:
Then I've clicked the Details icon and I got detailed information about the village - since when the registries exist and in which archives they are stored:
Now I know that I have to take a look into Prague archives (see Czech Archives on Internet for the link), Bykan (correct Czech version is Bykáň) parish to see if my ancestors were from this village called Chlistovice or from the second one the search engine showed me.
It's also possible to search for the villages directly on the archives websites. Unfortunatelly it's always not that easy as in case of GenTeam. Almost every archives has different system of searching for the village and parish. Anyway those archives which are not available in English, will be described here in future, so the "how to search for the village" part will be included there.