I always include speechbubbles in the thumbnailing stage! It's really super important to remember that you need space for words and stuff when planning layouts, as it saves you a lot of tears and extra work down the line. It's not a perfect method, since I thumbnail at a very small size and I don't always judge accurately how much space certain pieces of dialogue will take up, but at least it does leave me some space to play around with. Also, when I move to making full-size digital pages, I do the bubbles and the text right alongside my stick-figure rough sketches, so that I know for SURE how much space the text takes up.
I also edit my dialogue a bunch as I go, so sometimes I have to tweak and re-arrange the bubbles, but I'm usually able to pull it off without covering up important pieces of the artwork. I still need to polish my process up a bit - I still occasionally screw up and place bubbles in weird places - but I've still saved myself a lot of headaches.
... And yes, even though I include the speechbubbles right from the start, I always draw all the stuff that goes beneath them as well - I tend to want dialogue-free panels I can crop and use for promo-art.