Warning long - but this is a topic I find interesting.
I personally track my calories and my WW points every day. I also track my calorie deficit (amount burned less amount consumed) every day. Of all of these the calorie deficit is the only one that matters to me in the end.
WW points plus
To track WW points I use the WW site. I don't think there is any magic whatsoever in the WW points plus system. I think that using points rather than calories does 2 positive things. First, a LOT of people will not count calories. It is too much trouble and they just won't do it. They will count points plus though. Also, I think that WW somewhat gently uses points to try to get people to eat a more healthy diet.
Fruits and vegetables aren't "free" exactly. They are zero point. WW wants to encourage people to eat more of them. I know that when fruit had points I hardly ever ate it because I didn't love fruit at the time and I hated to spend points on them. Now that they are zero I eat them more often and have learned to really like some of them. All that aside the WW formula assumes that you are eating your 5 F/V servings a day.
As for other foods, WW gently disadvantages carbs and fats a bit and advantages protein. This is based upon the fact that the body burns more calories digesting protein that fat or carbs.
So for people who won't track calories and need help with healthy eating the WW points formula does work well.
However, because it is a formula you can't look at it as precisely as you do calorie. You can game it a bit to eat "more" food than you would eat under a strict calorie counting regime. Of course, you can game your mind all you want to but your body isn't gamed.
WW tries to do a formula, BTW, that creates a deficit of 1000 calories a day (i.e. a 2 pound weight loss a week) and assumed you eat a certain amount of zero point fruits and veggies. The formula falls apart at the lower point ranges because the formula also can't assign you so few points that you would eat less than 1000 calories a day. So the person who is at 26 points a day and is toward the lower end of the weight range (but still overweight) may not have a 1000 calorie deficit. WW also assumes a certain minimum level of activity (not including exercise) in coming up with that 1000 calorie deficit. For me, I know that on an ordinary day without exercise I don't hit that minimum level of activity so I'm not going to have a 1000 calorie deficit in any event.
Look up WW patent and some of the articles about it (Wikipedia has a good one) that discusses all this. This is also an informative article:
http://sockii.squidoo.com/weight-wat...-problem-of-29
Calorie counting
I also count calories on My Fitness Pal. The obvious question is why do I still do WW if I'm counting calories? There are a couple of reasons. First, I like that WW gives you daily minimum points (yes daily points are your minimum which you can add to with weekly points and activity points). But, you still get those weekly points. On My Fitness Pal I can set daily points but there is no way to set it to be an average of X points over a week. To me, it is unrealistic to think I will eat the exact same points each day. On WW I might eat 26 (my minimum) on some days and might eat 37 on another. But I can use my weekly points (and APs if need be) to make sure I stay overall in balance over the course of a week. So recording on WW is a good check to make sure I don't go over on a weekly basis. Like you, if my calorie count for the day is reasonable and I've eaten healthy all day then I don't worry if I am a point or two under my daily minimum occasionally. The key word there is occasionally.
Also, the big thing about WW for me isn't the points or the weight loss program. There are lots of ways to successfully lose weight eating in a healthy manner. What I like about WW though are the meetings and the accountability of the weigh in. When I consistently go to meetings I lose weight. When I don't consistently go I gain weight. End up story. So that is what I get from WW and points plus is irrelevant to that.
Calorie Deficit
Far more important than counting points plus or counting calories is looking at my calorie deficit. I have a Fitbit which tells me my calories burned (I do name some activities that the Fitbit doesn't measure well). MFP talks to Fitbit and tells it what I've eaten. I have a certain calorie deficit I want to have each day. I realize this isn't exact but it's close enough. Fitbit also tells me what my deficit is for the week. That is what I look at. I don't care how many calories I eat each day so long as I have the minimum deficit that I want to have (yes, yes, I work to eat in a healthy manner). The point is that losing weight is based upon that deficit and so I make having that deficit my mail goal. If I have the deficit and I've eaten in a healthy manner for the day then that is what I care about, not whether I've eaten X points plus.
And, I keep my motivation high and my goals short term by just focusing on each week's weigh in and meeting.