Using parsley and thyme in a brine I have a recipe for a brine that says to include a bunch of parsley when adding the ingredients to the boil. My question is, do I add the parsley whole, with the stems, or should I still separate the leaves? 

It also includes thyme so the same question for that, too.
In a brine, I would simply toss in the whole thing, stem and leaves, for parsley. In fact, parsley stems are quite flavorful. Thyme benefits from a bit of bruising to release the aroma and flavor.  So, I would roughly strip the leaves, not worrying too much if some stem was included.