C25K

Are you running outside or on a treadmill? When it's too cold/wet/windy to run outside, I use a treadmill, but then again my gym has shmancy ones that ask for your weight to calculate the calories burned more accurately. If the machine you use is lower-end, it may not be accurate.

If you're running outside, try plotting your workout on walkjogrun.com. Click "create route," let it find you (or find yourself if you're good at geography and can zoom in on your house/running area from space), and click along your path to mark your route. It's really easy. Then, in the bar along the bottom, you can click the little pencil icons by the various bits of data and tell it your actual speed, time, or pace; any one of those and it will automatically calculate the others. Click the pencil by Calories to input your weight, to get a more accurate calorie burn estimate. I find that this number doesn't change if you mess around with the speed and such, though, so I don't know how accurate it is, either.

If you can afford a heart rate monitor, that would be the best way to figure out how many calories you burn doing a C25K workout.

I add up all the intervals and log them as the chunks of total time spent walking and running. For example I am doing week 3 and it's 21 minutes walking and 9 minutes running so that's what I log (at the appropriate speed) plus I log any extra walking/running that I did seeing as I usually do abit more than just the program.