For new DJI products like the phantom 3 and Inspire 1, have a look at Map Pilot
http://www.dronesmadeeasy.com/Articles.asp?ID=254 from the guys who offer the MapsMadeEasy service.
The app is in beta stage and should be released in the near future. I have been lucky enough to be in the beta and the app is pretty rock solid.
If you can not wait for the app to be released you can manually fly in a grid pattern and snap photos manually as well. All photos taken with the Phantom3 and Inspire 1 are automatically georefferenced via the onboard GPS and ready to be processed inside of Photoscan.
After the "align images" step, you can add your GCPs to the project if you have them to bring up your accuracy. Then just continue on to produce a Dense Cloud followed by the mesh/DSM/Orthomosaic.
Alternatively to using Photoscan and processing yourself, you can also use an online service like MapsMadeEasy or DroneDeploy. I have tested MapsMadeEasy and it produces great results. I prefer to process locally though for more thorough accuracy and filtering.