To have your guitar properly intonated, is to basically have it 'in tune' at throughout the scale. Meaning, it's in tune at every fret throughout the neck.
Different string gauges, scale lengths, set ups, fret sizes, playing techniques and other variables can effect your instruments intonation.
If you ever wondered how come your amazing solo high up the neck never sounded exactly right, well, it's probably your intonation.
There's dozens of HOW-TO videos on Youtube teaching you how to intonate your guitar. It's easy, and very much worth learning.