Is your bottling wand something that's attached to a siphon hose that just dips into whatever container you're bottling from? If so, I'd dose the bottles and bottle from primary.
The amount of sugar to use depends on the type of sugar, the volume of the beer being bottled, the beer's temperature, and the level of carbonation you want. There are several carbonation calculators out there.
To reduce risk of contamination, the sugar should be boiled. If you just add it straight (dry), there's an additional (small) risk.