The point of having the 'default' calories (resting/sleeping) is so that you can see what kind of calorie deficits you are creating. Obviously this won't be an exact science, but it should get you pretty close. If you think it is overestimating your base of calories burned, you can always change it to 24 hours of sleeping, which should come out to be the lowest possible numbers of calories burned without exercise. If you zero it out, then your calculated calorie deficits will be enormously overestimated.
And like johnnybadback said, you can always select the "other" option for entering exercise/calories. I pretty much always use that as my option for entering my calories burned as recorded by my heart rate monitor. You're right, FS typically overestimates the calorie burn for many activities.
Someone who is busier than you is working out right now.
There will come a day when you can no longer do this. Today is not that day.