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The official motorway website for Czech Republic offer some details on what parts of the motorway are charged and which are not. Most petrol stations sell them and you can ensure you go past one by using one of the following:
When entering the Czech Republic on motorways D1 (from Poland near BohumΓn), D2 (from Slovakia near BΕeclav), D5 (from Germany near Rozvadov) and D8 (from Germany near Petrovice), the sticker can be bought on the first rest area after the border. (source)
If you enter the Czech Republic by one of the free motorway areas, or a non motorway road, you can also buy them at most post offices, but unless it is in a city or large town they might not take card at all, or unless you spend over a specified amount.
Note that Road and Motorway Directorate (ΕSD) does not have its own selling points.