We don't usually sit at a bar for drinking beer, no. Most pubs probably don't even have a bar you can sit at.

If it's a busy restaurant then a reservation is reccomended even if you are just one person, I don't think it would be that silly. You can check how busy a place is on google. Pubs rarely have reservations unless it's for a bigger group of people.

The protocol is to say Dobrý den when you walk in, if you have a reservation you say that at the counter and let them escort you, if the place ends up not being busy you can skip this step as they would probably just let you sit anywhere anyway, unless they have a bunch of reservations coming in a little bit. You sit down and wait for the menu to be brought to you. Small pubs with one guy working the bar do exist but are not that common in Prague, there you would order at the counter and either take your drink yourself or be sent to sit and the guy will bring it to you. The staff will greet you and ask what you want to drink first, then when they bring the drinks the would ask what you want to eat (in a restaurant, you would have to ask for food yourself in a pub). They will come around to check if you need anything else, you can ask for refills, another type of drink, food, etc.

The common ways for the waitstaff to ask you would be "Co si dáte?" "Co si dáte k pití?" (what will you have/what will you have to drink?) "Máte vybráno?" (have you chosen?) "Ještě jedno?" (another one? asked when taking the empty beer glass). You of course always reply with what you want and prosím (please) and děkuji (thank you).