Sixes explode with Edge spent on extra dice. Spent beforehand they ALL explode. Spent after only the Edge dice explode. If you have a large dice pool then you get more bang for your Edge buck by purchasing the reroll; you get another chance for 5's and 6's to hit instead of just 6's.
First, only dice that didn't score a hit (4 or lower) are rerolled.
Second, Rule of Six only applies when you spend edge to add dice (all dice, if spent before, edge dice only if spent after rolling).
Read the Spending Edge section, the Rule of Six is explicitly invoked when it applies. They make a point of reminding the reader that the Rule of Six doesn't apply to a Long Shot test, because a Long Shot test, when described in full, talks about rolling your edge dice (where the Rule of Six normally applies). The Rule of Six is not invoked for re-rolling misses.