How does one accomplish this while avoiding skyboxes?
You need to Jump, Double Jump (jump in mid air), then aim the Force of Nature (FaN) at the ground and fire.
This will give you another "jump", thus the triple jump. There is extremely little chance of you hitting the skybox as they tend to be very high.
It's also worth noting that the scout will often woop/cheer when you do this :)
The Force-A-Nature doesn't provide you with a high vertical jump like a rocket jump does for the soldier, so you needn't worry about hitting skyboxes.
For some fantastic ideas on triple jump locations, this video is a must-watch: