The points thing is nothing but a guide, you can be up on points but losing the game.
If you have enough material to checkmate and your opponent runs out of time you win, no matter how badly you are losing on the board. If you don't have enough material to mate (lone king, King&bishop, King&knight) it's a draw.
How does the 'won on time' rule function? I took an opponents Queen and I'm pretty sure I was ahead on points when suddenly the computer announced that my opponent 'won on time'. An explanation of the rule will be appreciated.