This going to be driven partly by the specifics of what you're designing for, but there's a sort of rough heirarchy to these things in, say, a typical blog index:
- You're going to have one footer on a page.
- You're going to have one header per entry.
- You're going to have n paragraphs per entry.
Establish whitespace for your paragraphs knowing that they're going to sometimes occur in sequence -- you need to worry about how they look as a series. From there, adjust your headers to deal with boundaries between entries. Finally, adjust your footer/body spacing to make sure the bottom of the page looks decent.
It's a thumbnail sketch. How you ultimately end up assigning your padding is entirely up to you, but if you approach it from an bottom-up perspective you'll likely see less surprises as you tweak first the most common/plentiful elements and then later the less common ones.
