Often you cannot guess what a word means by the root, but the root can help you to remember it. So for instance להגדיר means "to define." It is related to גדר, "fence." So you can think of defining a word as fencing in its meaning. Or you might remember לפנות, turn to, because it is related to פנים, "face."
You can take this too far, though. You might look at צלחת, "plate," and try to connect it to להצליח, "succeed." If you see the logic in this, I commend you, but sometimes I think there really is no connection, or it has been lost.
Sometimes there is a single root that has two completely different meanings, though. The classic example is ספר. In some words, this relates to "telling," like סיפור and סיפרות. But in other words it relates to cutting hair, like תספורת and מספרה. So you have to be careful, because the root can sometimes deceive you, as well.