You can modify certain colors as the colors of the
theorems, lemmas, etc..., and also the background colors of
the theorems, lemmas, etc...
In order to do this, you go in the menu Preferences->jPreTeXPreferences then you choose Couleurs then for instance Couleur de fond theoremes ; finally you choose Theorem, lemma, etc... Then you have a palette of colors and you choose the one you want.
This allows you to have different sets of colors by directories of your documents.