I am with estela, if it is cold and particularly dry out, go with evergreen bedding and skip the smudge. Natural repellents such as paw paw are great repellents to line your bedding with. Do a search of natural repellents in this forum, I know there are a few threads. Regardless, the debris you are using for insulation should be dry which inherently will have very little pests. However, if you have the need to smudge...
Put some coals on whatever you can find (sheet of bark, large evergreen broadleaf, whatever - put dirt on it first if you think it will burn). From there you can smudge your shelter by putting the herb of your choice on the coals. The most popular smudge is probably cedar which is more of a repellent, however, I would imagine anything that smokes would drive off or kill most bugs. Obviously, steer clear of poison ivy, etc. I would also avoid smoldering wood from the campfire as it being linear and somewhat round is asking for trouble as it moves to readily.
Haven't done it enough to tell you how long before, etc. However, common sense tells me to do it with enough daylight left to adjust should something go wrong and the majority of that decision depends on the weather (past and present), materials, and surrounding environment. A lot of variables with this, for example, I wouldn't think it out of the ordinary to smudge everyday if you were in the deep south in mild temperatures.
Let us know how it goes - good luck.