Typical PVC rigid pipe with holes comes with a pair of rows of holes down its length. If you are running this pipe say, along your foundation's footer, or through a wet area to drain the water away, how do you place the pipe?
Well, it would appear that common sense says holes pointing up. You wouldn't want the water to drain out again would you? Well, this is one that is counter-intuitive I guess, because the holes go DOWN. Consider the saturated condition of the soil or sand or stones around the pipe.. in order for the water to get into the pipe, the water level has to reach the height of the holes. You aren't really trying to catch the small percentage of the water that might luck out and drop right into a hole.. what you are doing is draining away the water as the level rises to the height of the holes in the dirt or ditch or where ever you have placed the pipe.
So, holes go down, then basically the water level in the area around the pipe will be at the bottom of the pipe instead of at the top.
If your old shingles aren't curled you can nail new shingles directly over them. If you already have 2 layers, then its best to tear them off and start over. Any time you suspect damage to the roof deck below the shingles you should tear off and inspect and replace the plywood as necessary.