There are two way to get to Manu:
It is possible to enter by a combination by bus and boat and leave through the same boat/bus combination. This option can be a long trip.
By plane from Cusco arriving directly to the jungle lowlands It will take about 40 to 45 minutes. InkaNatura is offering flights five times per week using a Cessna Grand Caravan. (http://www.inkanatura.com...)
It is also possible to use the combination of travelling one way by bus/boat and the other by plane.