Hi David,
I went to Prague a few time many moons ago now and enjoyed each visit very much.
Presuming this is where I went, as it is the only photography museum listed on google, it is well worth a visit and will take you out of the tourist bubble for a few hours as it was just out of town in a residential area, but easily found on a tram / train line:
http://en.ghmp.cz/house-of-photography/
Something new that has opened since I went there is a Leica Gallery, which is right in the centre it says:
http://www.lgp.cz/en/about-us/the-gallery.html
As for food, I too like to eat what the locals do and it is quite easy to find places, although I got a few looks going into some of them, just for being a tourist - obviously not many of us go into the places.
Don't overlook the tourist bits though as they are worth visiting. I remember a museum of torture at the Charles Bridge and a fun fair on a hill close by that had a maze of mirrors which was fun.
A good look on google or a good guide book to browse before you go are very recommended as most people only stay in the centre of town, which although lovely there are other things if one looks.
What ever you do, I'm sure you will enjoy yourself.
Terry S