From Prague south to the Danube River, we more or less made up our own routes, with the use of large scale cycle specific maps we found available at bookstores and tourist offices in Prague and the rest of the Czech Republic. There were many routes to choose from, and we generally took routes that followed the Vltava River valley. The maps had topographic contour lines, so we were able to avoid many "unnecessary" climbs, and we also knew when climbs were inevitable. These maps were invaluable, and well worth the money we spent on them.
You can pre-order the maps by following the link here: Czech Maps

MAP OF EUROPE SHOWING CZECH REPUBLIC - CLICK ON THE GREEN FOR A MORE DETAILED MAP

THE ROUTE OUT OF PRAGUE ON THE GREENWAYS BIKE ROUTE
OUR ROUTE WAS SLIGHTLY WEST OF THE ONE SHOWN HERE, AND CONTINUED SOUTH FROM CESKY KRUMLOV TO LINZ

THE DONAURADWEG - THE DANUBE CYCLE ROUTE
START PAGE - CYCLING PRAGUE TO VIENNA