I don't like sugar rubs. But that is a personal thing. If you like rubs with brown sugar, honey or whatever, I would think that you would put it on in the beginning of your smoke. I personally like more spicy rubs than sweet, but I always want my rub on at least an hour before it hits the smoker. :D
For long cook items, you don't want too much of the wrong kind of sugar but in moderation some of the right kind is fine from the beginning.
You put sugar in rubs for 2 reasons, sweet taste and bark development. The caramalization of sugars is what causes the spice mixture to crust up and develop bark.
You can achieve this by adding sugar at the beginning or using a sugary spray/mop later in the cook.
Different sugars stand up to extended heat in different ways.
Turbinado sugar (sugar in the raw) stands up to extended heat best, so is a good choice in brisket and butt rubs.
For shorter cooking items like ribs, brown sugar is fine, I like dark brown sugar on my ribs. I rub my ribs with the dbs then apply rub that has sugar in it too. Then add sweetened apple juice (brown sugar and honey) to the foil if I wrap or spray it on.
I like spicy rubs, but if you add a lot of heat, adding sugar will help to temper the heat down to a nice warm finish instead of allowing it to be overbearing. Also with spares, the sugar mellows the stonger taste of the pork from lower on the hog.