The CTM bus company (their bus is pictured here) has an office in the main bus station which is situated down the hill from the medina in Chefchaouen. You can purchase tickets in advance to most destinations within Morocco.
It takes about 4 hours by bus from Fes and Meknes to Chefchaouen (and costs around 70 Dirhams). It took us just 6 hours to get from Chefchaouen to Casablanca (there's only one bus, leaving in the morning). Private bus companies run to most other destinations not covered by the CTM company, and most drivers and owners will be milling around the main bus station. Get to the bus station in the morning for most departures.