Sure, it can be done. It's an iFly! :-)
Click Menu in the lower-left corner of the screen, then Custom Waypoints, then Create New Custom Waypoint.
Make sure you select decimal, deg/min, etc. properly, name it what you want, and put in your numbers.
When using custom waypoints to build a flight plan, just make sure you've got the "Find Custom Waypoints" checkbox selected.