What will it do from take off? Let's say I set my first way point at 400 ft 2000 ft away from launch. Will it make its way there at a calculated incline or raise to 400 ft at launch point then head to 1st way point. I'm contemplating doing a one way mission and landing there.

If your second point has different altitude, the aircraft will reach that altitude automatically.
Please correct me if I misunderstand your description.

Just make your first waypoint at 400 ft above the home point, then the 2nd waypoint at 2,000 ft away. Then you won't have to worry about how it does it.