Jess,
You can use something like the AOPA Flight Planner to build a route and then export to a GPX file. Save that to a USB stick, and then you can load that flight plan to the iFly device from the "Load" button on the Flight Plan page. This will not work for the App yet.
Currently there is no way to import a list of use waypoints, this is on our wishlist for consideration in a future software update. We are also looking into a sync or cloud based solution in the the future to backup, save, etc of the functions of your software. This could also be a nice place to import, then just pull them down to the device. It would also resolve the GPX file transfer for the App as mentioned above. Stay tuned.
As fo exporting past flight, you can copy them from the SD Card, they are in the Log's folder inside the User Folder. Currenty there is no way to export them from within the software. This is also on our wishlist.