All hotkeys are set via the Keybindings menu. Look for the Bongos section for the majority of them.

Actionbar
ActionBar 1 uses the same hotkeys as the Blizzard main actionbar. In the keybindings menu they are under Action Bar Functions. The rest of the hotkeys are listed as Bongos Actionbar <Bar Number>.

Pet Bar
The pet bar uses the same keybindings as the Blizzard pet bar. In the keybindings menu, they're listed as Secondary Action Button.

Class Bar
The class bar's hotkeys are the same as the blizzard ones. In the keybinding's menu, they're listed as Special Action Button.