First, a note on "compatibility" (for want of a better word). This piece is written after some extensive theming work in Ubercart 5.x-1.7. Much of this is still useful information for the Drupal 6.x version of Ubercart, but it may not be wholly accurate.

I should also note that this is not really a hand-holding step-by-step piece. It's more for people who are already pretty familiar with theming Drupal and just want to know where to look.