"There are birds sitting in the window."
Translation:Na okně sedí ptáci.
"Birds are sitting in the window" would translate to "Ptáci sedí na okně."
This is the difference between telling "The birds are somewhere" vs "There is something in the window." In other words, it answers a different question:
"Where are the birds? - The birds are in the window."
"What is in the window? - There are birds in the window."
"So-called free-word order languages (e.g. Russian, Czech, to a certain extent Chinese and German) use word-order as the primary means. Usually the topic precedes focus. For example, in some Slavic languages such as Czech and Russian both orders are possible. The order with comment sentence-initial is referred as subjective (Vilém Mathesius invented the term and opposed it to objective) and expresses certain emotional involvement. The two orders are distinguished by intonation."
I see the tendency of many people to put the verbs last. However, Czech is not Latin. It does work in specific contexts, but in many it does not. It is not the neutral order. It makes the verb the focus of the sentence.
Na okně ptáci sedí. - Birds (do) sit on the window.
That is a reply to someone saying that birds do not sit on the feeder. And even then you can as well just say "Ptáci sedí na okně.".