The Unbearable Lightness of Being by Milan Kundera (1984) is set in Prague and the Czech countryside during the Soviet-era occupation, and it is the novel that most completely captures a certain Czech sensibility — ironic, melancholy, resistant. Kundera wrote it in exile and it was banned in Czechoslovakia until 1989. Reading it before or after a visit to Bohemia gives the landscape and history a depth that no guidebook can.
The Good Soldier Švejk by Jaroslav Hašek (1921–1923) is the great Czech comic novel: an anti-war satire following a cheerfully idiotic soldier through the chaos of the First World War. Hašek was himself from Bohemia and the book is deeply rooted in Czech culture, humour, and a particular kind of stubborn pragmatism that you will recognise everywhere in the country. Unfinished at the author's death, but worth reading for the completed sections alone.
A History of the Czech Lands edited by Jaroslav Pánek and Oldřich Tůma (2009) is the most accessible scholarly history of Bohemia and Moravia in English, covering two thousand years from the early Slavic settlements through the Habsburg era to the present. Dense in places, but essential context for understanding why the castles, churches, and town plans look the way they do.
Šumava: The Wild Heart of Europe — various natural history and walking guides exist for the Šumava (Bohemian Forest) region that borders Český Krumlov to the south and west. The landscape is one of the best-preserved in Central Europe, and a decent trail guide will open up the day-trip options considerably.