I read the San Francisco Chronicle online. When I visit sfgate.com, the corresponding website, I'm assaulted with a popunder advertisement. It's just a white box that I end up closing because of AdBlock. How do I configure AdBlock to block anything from "http://www.sfgate.com/templates/types/popunder/,' seeing as anything from that URL is in the page source of the offending popunder scripts. (Alternatively, is that even the correct way to go about blocking those popunders?)

i don't think adblock itself can do it; without looking at the source i'm guessing that (as is usually the case) this is javascript's work, and adblock can't block that (if it's part of the current page's source).
still, you can always neuter javascript. most major browsers should have domain-specific policies, and a 'do not allow spawning new windows' button, or the like.

I think Adblock only blocks in-line elements, if that's what they're called. Pop-ups/pop-unders have to be blocked by some other tool.