Hi Scoobyfanatic!!! Welcome to 3FC!
I use Myfitnesspal myself to count calories, and I love it! My goal is 1200 a day, however I tend to be balanced more between 1000-1200 (I know its low, but I'm not hungry and I watch the essential nutrients to make sure I'm getting enough, and take vitamins) depending on my activity level. I also use a Fitbit One to measure all of my movement so I can gauge how much I actually burn throughout the day. I did Weight Watchers for 2 months and had the same issue you did, where I wasn't losing at the rate that I thought I should be able to, and I found that with the free fruits and vegetables I was eating around maintenance level calories instead of deficit, so that's when I switched to calorie counting so I could be more accountable for what I ate.
One of the big things I'd say is don't start with the lowest calorie intake possible (I don't think myfitnesspal would let you go below 1200 calories). I had gotten used to smaller portions from weight watchers, so it wasn't so hard to ease myself into calorie counting, but if you have been eating larger portions for a while, it would be easier to start with something like 1700 calories for a week, then 1500, and so on, just so that you don't feel like you're starving yourself.
I'd also recommend a food journal. I keep track of the calories in Myfitnesspal, but I keep a food journal at my desk so that I can record things like my mood, scale fluctuations, etc. I weigh daily, and compare what I ate the day before to the scale and see if there might be any foods to trigger gain. I also look for emotional triggers...I simply cannot have a pint of Ben & Jerry's ice cream in my apartment. I just can't. When there's one in the house, if I get even the smallest mood swing that is the first thing I grab, and I can easily eat half if not all of the container in one sitting.