I don't know about other calorie counting sites, but on FitDay, activities are measured by calories burned per minute, so they count the calories the same whether it was 5 minutes or 5 hours, so it wouldn't matter. When I do similar activities (such as weight lifting) more than once per day, I like to enter it more than once, because it helps me track my activities more easily, though.
220 pounds - 6/15/06 - most recent weight prior to start of diet
Start Date - 5/30/07
200 pounds (20 pounds lost) - 7/2/07
190 pounds (30 pounds lost) - 7/30/07
180 pounds (40 pounds lost) - 9/4/07
Body Fat Percentage: 36.1/28.4/15
= 5 pounds lost