I am a regular visitor to Prague and the food and drink scene is always changing,a few of my favourites.
http://www.pivolod.cz/v2.0/
this is a new place on a boat on the river and is excellent.a nicro-brewery that has up to six beers available.
it also does great food,Top deck is a grill area,main deck a proper restaurant doing Czech Classics in a modern style,I can highly recommend their Duck and rabbit dishes.
lower deck is a proper pub with a limited beer food menu (worth looking up beer food as most pubs will have this available.
http://www.podjuliskou.cz/en/
on the northern boundry of the city last stop on tram8 and 18 (Podabada), great food more bistro style but good choice was in there twice at the beginning of the month and it was excellent, I often visit there when in the city as I have a friend who lives nearby and it is basically his local.
https://vytopna.cz/pages/vaclavak
this is on wenseslas Sqaure,not the greatest restaurant but a real fun place, does half decent pizza but the little trains that deliver your drinks are real fun,there is a cover charge in this place but the do tell you when you go in it is only 20kc so nothing much.
http://www.restauracebredovskydvur.cz/restaurace/en
this place is on a street parallel to Wenseslas Square, great food and you actually watch them cooking it, great beer from the tank,I can highly recommend the venison in there.
http://www.u3r.cz/en/
In the heart of the Old town,a micro-brewery that does about 6 beers, food is excellent and the décor is quite lovely huge murals on the walls as well as some eclectic Czech paintings
http://www.cafelouvre.cz/en/
this is a stunning place though I have never had an evening meal there I often meet friends there for a late breakfast or for coffee and cakes, looks a bit dodgy from the front but once inside it is truly beautiful.
that gives you a few idea.
https://www.kolonialpub.cz/
this is opposite the Old Jewish cemetery does great ribs and chicken wings and excellent beer,try the rezane beer, dark beer floated on top of light beer,bloody lovely.
there are a few chain restaurants I can recommend.
Lokal ,Potrafena Husa and Kozlovna chains have various places throughout the city I have eaten and drank in many of them and never had a bad meal or indeed a bad beer, prices have always been reasonable and service great.
worth ducking down a side street to see what is there and giving it a go you just might find a real winner.
hope this all helps.