I've used fitday years ago, but don't remember if that one subtracts exercise calories or not.
Calorieking does, but I'm assuming you want free sites, and that one costs an arm and a leg now.
Sparkpeople definitely does not
- although it DOES keep track of exercise calories so you could easily subtract it yourself if you wanted.
Other sites you may want to check out: www.my-calorie-counter.com
Then again, if Livestrong's site is too confusing, I'm not sure any of these other ones will be any easier - calorie tracking is always the same process... you search for a food or exercise, you enter a duration or amount, and you watch the numbers add up.
Personally, I find livestrong/dailyplate and sparkpeople to be the easiest to use, because they've got enormous user-generated databases, so I almost never have to enter things manually. I remember using fitday and entering almost every food I ate manually (of course, you only have to enter it once).