Praha is the capital of Bohemia ?
Bohemia is the western part of Czechia. Prague is the capital of both Bohemia and Czechia. The sentence here uses "Česko", the Czech word for Czechia, not the word for Bohemia, which is "Čechy".
So you do not use one word for the capital, you have to use it with mesto always?
Yes, it simply means "main city".