Depends on your goals and what exercises you plan to take up. Jogging thin, regardless of -fitness-, is a -hell- of a lot easier than jogging fat. It's also less likely to cause you injury, speaking from personal experience.

If you're severely overweight to begin from that's unlikely to be much of an issue. See Desrtopa.

(ISTR someone -- was it Beeminder's blog? The Hacker's Diet? [EDIT: here it is] -- recommending tracking body weight because it's so readily quantifiable until you're in the ballpark of your ideal weight, but to switch to something better if you want to keep on improving afterwards.)