i was up to bat and there was a guy on 1st adn 2nd . the pitcher lifted his left leg up then my guy on second began running to third well the pitcher saw this and then directly threw it to third the umps didnt call it a balk, now im not an ump but i thought a pitcher cant throw to an unoccupied base

That's legal, because he's throwing there to make a play on a runner.

well u can if the runner is going to the unoccupied base but if the pitchers leg crossed his other leg ( meaning that the foot came across his body) than he must throw it to home plate

It isn't considered a balk unless the pitcher made a move to throw towards home and then changed at the last second to throw it to 3rd. Throwing it to an empty base has nothing to do with it.

Rule 8.05
(d) The pitcher, while touching his plate, throws, or feints a throw to an unoccupied base, except for the purpose of making a play;

The key here is except for the purpose of making a play, since the runner is on the way to third, the purpose of his throw is making a play, not a ruse or a fake, therefore, it is a legal play.

He was fine in doing so as long as he didn't stride to the plate.

A pitcher can throw to second, third or the batter from a wind up or stretch. He cannot throw to first without first taking his foot off the rubber. Hope this answers your question.

And how else was the pitcher supposed to try to get the out at third? The runner was on the way to third, after all. He's not allowed to throw to an unoccupied base EXCEPT to make a play.

Rule 8.05 (d)

It doesn't matter where the pitcher throws the ball. What draws the line between a pick off move and a balk is the pitcher's footwork. If the pitchers foot begins moving towards the plate, a stop and change to pick off a runner is considered a balk. Otherwise, it's a pick off.

If the umpire determines that the foot (1) did not start to home plate, (2) was in a continuous uninterrupted motion and (3) was directly at third base the play is legal.

I had this a few years ago and ejected a player and pitching coach for my trouble.