Huasipungo by Jorge Icaza (1934) is the landmark Ecuadorian novel — a brutal, unsparing account of indigenous labourers on a highland hacienda being driven off their land. Published in Quito and set in the Andean highlands, it remains essential context for understanding Ecuador's social history and the exploitation that underpinned the colonial and hacienda economies visible in the architecture of Cuenca.
The Old Patagonian Express by Paul Theroux (1979) traces a train journey from Boston to the tip of South America, passing through the Ecuadorian highlands. Theroux's observations of Andean towns and landscapes in the late 1970s are vivid and often acerbic — good reading on a long bus ride south.
The Inca Empire: The Formation and Disintegration of a Pre-Columbian State by Terence D'Altroy provides serious scholarly context for the Inca occupation of what is now Ecuador — the northern limit of Tawantinsuyu, and the region where the Inca civil war that preceded the Spanish conquest was largely fought. Useful background before visiting Ingapirca.
Lonely Planet Ecuador & the Galápagos Islands — the standard practical guide, useful for logistics across the country. Cuenca is covered in enough depth to help with orientation and current restaurant and hotel listings.