I've done both. A Mr.Beer kit I used had me add the sugar directly to the bottles. On a small batch like that it may work, but a little bit of sugar being off can result in one bottle being full carb'd, and another being flat.
Generally what most people recommend here is taking you priming sugar (usually 1/2-3/4 cups of corn sugar), putting it in 2 cups of water, boiling the whole thing, then cooling it, then gently stirring it into the beer. Then into bottles. Generally you do this whole part after you've racked into your bottling bucket (sanitized right?).
Most people recommend against stiring the priming sugar directly into the beer, then bottling. Reason: Sugar isn't sanitized (boiling takes care of that) and you may have something that I (and many others have done)... the sugar doesn't full dissolve so you have a small layer at the bottom that doesn't get mixed in and the overal sugar is lower so you end up with flat beer for a while (it may eventually carb).
So not an entirely n00b question and has many points. All aspects would work just fine and will work, I just described the IDEAL situation.