Don't worry about the sugar. I've done lots of 'not boiled' sugar. Natively, sugar is to dry for bacteria or mold to grow on, that's why we throw it in our cupboards and not a fridge.
Yes there could be a few bacteria from processing in with the crystals, but the quantity is going to be over taken by the yeast.
As for the process, you can put the sugar on top or on bottom, BUT I think the easiest is to disolve and boil and then syphon the beer on it as described by mcangeli.
Much easier than trying to measure a tiny bit and put it in each bottle. OR you can use carbonation tabs, which are basically little sugar pills about the size of a cough drop. I think 1 per 12oz bottle.