SueQ: The computer will not mark all dead stones for you; you should do your best to mark them on your own, and once both players agree the game is done.

The reason it's done this way even on the fanciest Go servers is that it's often very difficult for the computer to tell whether stones are dead or not. There are various rules that can be followed, but the complexity of the problem exceeds most Go software even today. However, people are generally very good at finding dead stones (compared to computers) and so there's that last bit of manual work required to correctly score the game.

SueQ: Fwiffo is right...it will take a little while to understand the eyes concept and life and death of groups, but you'll feel it happening. Go is a beautiful game and a lifelong pursuit, but you can see yourself making progress from the first day.