Do I sand just the bubbles or the whole epoxy surface before recoating?

Either. You have two options, and the choice is yours.

Spot fix: Sand only the areas with bubbles (or the burned spot), finishing with 220-320 grit, and wipe them clean with acetone or denatured alcohol. Mix a very small batch of UltraClear Bar & Table Top Epoxy and paint it over the sanded areas with an artist's paint brush. Dip the brush into the center of the container so you pick up fully blended epoxy rather than unmixed material from the sides. Some customers have great success with this, but there is no guarantee: the repair can leave a seam and a noticeable difference where new epoxy meets old.

Full re-coat: The only way to get a seamless finish. Sand out the bubbles, then scuff-sand the entire surface with 220-320 grit, clean it all with acetone or denatured alcohol, and pour a new flood coat over the whole top. You do not have to sand the entire surface down, only the spots with bubbles; the rest needs just the scuff. The self-leveling flood coat levels out across the surface, fills the sanding scratches, and leaves a glass-like finish with no seams, as long as it is mixed and poured correctly.

Whichever you choose, be careful not to sand through to the wood. Exposed wood needs a new seal coat before any epoxy goes back on, or bubbles will rise into the fresh coat.