Flying to Pokhara from Kathmandu ensures that you spend as little time traveling as possible. With a flight of less than 1 hour, you can be in Pokhara on your way to Annapurna or relaxing Lakeside with a cocktail in hand before a bus would even get out of Kathmandu Valley.
The flight departs from Tribhuvan Airport in Kathmandu. This is likely the airport where you arrived in the country. There is a domestic terminal specifically for flights within Nepal. Flights to Pokhara run frequently throughout the day providing good weather.