The ride from Bratislava to Prague was mostly on freeways with roadworks for more than half the way which is why it took 3:50hrs to do 332km. The border was a non event, no signs or anything to say you had crossed a border. No tolls or vignettes for bikes in Czech.
Prague is a big city 1.3 million, it has a metro 3 lines, trams and buses, not many English translations which considering the number of tourists is not very helpful. There are literally herds of tourists being led around by guides, many from Asia as well as Russia and neighbouring countries, very annoying until you get used to it and if you get away from the main attractions its a nice place.
I discovered this website which has walks for a number of cities and followed the Prague walks, very good, http://www.use-it.travel/home
Tip – Tram 22 takes you to the top of the hill and from there you can walk down to the Castle or the Monastery or to Petrin Tower. I walked up the hill twice before I discovered this and used it for the next two trips.