You shouldn't put your sugar into each bottle. For one, this method is less reliable in terms of how much gets into each bottle. Secondly, I would not use sugar for priming, although you will find a number of brewers posting after me who will claim that using sugar is absolutely fine. I will let them tell you how much to use.
Here is what I do to bottle. I boil 1.25 cups of Dried Malt Extract with a bit of water - a couple of cups. Then I cool this wort and put it into the bottom of my bottling bucket before I siphon my beer into it. After I siphon the beer onto my priming sugar "wort," I give it a good stir with a sanitized spoon. Then, bottle.
This method - even if you decide to use sugar - will more evenly distribute the sugar in the beer.
If you use priming sugar, I believe that you should use .75 cups - three fourths of a cup, but you should get a second opinion on that. It has been years since I've used priming sugar.