It depends. If you are going to temp orally, go ahead and start on the first day of heavy flow (enough to need a pad/tampon). I temp vaginally so I wait until my heavy flow is over or I'm just spotting to temp. I keep a box of alcohol pads on my nightstand and wipe the thermometer down after every use.
If you are a mouth breather, you will get more accurate temps from temping vaginally. If mouth breathing isn't an issue and you haven't noticed erratic temps, then oral temping is fine.