Thanks to the World Cup, I Have Some Soccer Questions

Having not followed soccer closely, I found myself watching the game between Portugal and the USA and asking some questions along the way.

I was under the impression that the game would end at the 90 minute mark, yet it didn't. I found out the the referee has discretion to add time to the clock and extend the playing time beyond the 90 minute mark. Apparently it is a culmination of time from all the stoppages during the game. My question is, why don't they stop the clock and resume it after a stoppage? That way everyone knows exactly how much time is left in the game. This seems archaic to me.

The other question I had is this: These guys run about 8 miles a game, yet I never see them getting a water break. Are they coming to the sidelines off camera and I am just missing it while play is continuing?

I believe I also heard that some of the rules of the game will change when they get to the next round of the World Cup. What rules will change? I am trying to learn the rules of soccer, but if they are going to change the rules as we go along that might make my task difficult.

I can answer just about any question regarding baseball but not soccer. So soccer fans, I could use some answers. Thanks!