Take a look at any large corporation's balance sheet. They usually have short-term cash (basically bank accounts) and short-term cash equivalents (very liquid assets like gov't bonds).

So basically you are correct. The CFO devises a plan to pay that fine by pulling cash from a number of different sources.

I also assume that the gov't is paid with either a single payment or a couple payments. I can't remember the context in which I saw it, but there was a copy of a check posted on a website for several billion dollars. Looked like any other corporate check (with a few more signatures on it).