If it's for Cyanogen or some specific ROM then it most likely will not work with BB. The latest BB is built from FRF84 (I believe) and most of these other ROM's like Cyanogen are built from source code. Because of that they may have different file structures which will cause certain themes to not be compatible between them.
If a theme works for BB it should be listed as working with BB. You may also be able to get away with using themes that are designed for regular old FRF84, but because Pete may or may not include different apps in the system partition, the theme may not apply properly either.
Generally it's best that you apply a theme that is proven or designed to work with a specific ROM. Of course you could always just make a backup first and play around with things to see what happens.