During two-games developing I have found one useful solution.
It's nested-clocks - simple java-class for managing of time-threads.
Main idea is that if you pause clock then all children clocks will be paused too.

public class GameClock {
	
	private boolean paused = true;
	private long startedTime = 0;
	private long pausedTime = 0;
	private GameClock parentClock;
	//create top-clock, without parent
	public GameClock() {
	}
	//create nested-clock
	public GameClock(GameClock parentClock) {
		this.parentClock=parentClock;
	}
	//just for comfort, easy way to get time in parent clock
	private long getParentTime() {
		if (parentClock==null) return System.currentTimeMillis();
		return parentClock.getTime();
	}
	//getting current time
	public long getTime() {
		return (paused?pausedTime:getParentTime()) - startedTime;
	}
	//setting current time to zero, and starting clock
	public void start() {
		paused = false;
		startedTime = getParentTime();
	}
	//pause current time
	public void pause() {
		if (!paused) {
			paused = true;
			pausedTime = getParentTime();
		}
	}
	//resume current time
	public void resume() {
		if (startedTime==0) start();
		if (paused) {
			paused = false;
			startedTime += getParentTime() - pausedTime;
		}
	}
	//sleep in current thread, using non-system time but this-clock time
	public void sleep(long mlsec) {
		long now=getTime();
		while(getTime()-now<mlsec) {
			try {Thread.sleep(mlsec - (getTime()-now));}catch(Exception e) {return;}
			if ((getTime()-now)<0) return;
		}
	}
}