You're pretty much on track. The basic idea of calorie counting is calculating the number of calories in the amount of whatever you just ate, then keep a running log of the total for the end of the day.
You don't have to go by the specific serving size listed on the package, but it's a useful guide. For your example, you can measure out 1 c of popcorn, then log that into your calorie counter. It will probably automatically generate 45 calories to add to your running total.
If you want two cups of popcorn instead of the recommended one, that's fine, just log it. That's the beauty of calorie counting- it's very flexible. As long as you are eating balanced food and getting in your nutrients you can eat what you feel is best for you
For homemade food, you can either a) search your online calorie counter for a similar product (i.e. search for homemade chili) and log that or b) like Jenneo said, use the "recipe" function to input everything you put into the chili and calculate serving size. Option B is MUCH more accurate, but it's more time consuming. What I usually do is take the time to calculate recipes I use a lot to have an exact amount, and then for food I've had at someone else's house or something like that I'll do the search feature to find similar recipes. Sometimes searching for a recipe with the same name works, sometimes it can be woefully inaccurate. Use your common sense. If you just baked a cheesecake that you know has tons of calories and the already-inputted cheesecake entry that comes up in your CC gives it 150 cals and 5 g of fat, you may want to look for a different entry.
Also, if you cook using online recipe sites, like AllRecipes.com, they often have the calories, fat, protein, etc already calculated on the site. You can just use those.
Measuring and weighing are really important for calorie counting. Don't eyeball portions of meat, cheese, cereal, pasta, etc. Measure it out, at least for the first month or so. Again, takes time, but you'll get a much more accurate calorie count. Otherwise you will likely- as we all have!- assume what a cup of pasta looks like. only to be shocked when you finally measure it and found you're eating 2 1/2 cups!.
If you are at a party or out somewhere and can't measure, it never hurts to overestimate the portion size when you get home and input the cals. If you think you ate 4 oz of chicken parmesan, input 6.5. That's my rule of thumb, at least. I usually increase what I think the portion is by about 30%. Because you don't know what's in that food (and restaurant food has lots of hidden oil, butter, etc) and the portion, overestimating a bit has tended to give me a more accurate calorie estimation (as evidenced by on-target weight loss).
Like Jenneo said, calorie counting takes a bit of time upfront, but once you get the hang of it it probably wont' take more than 5 minutes each day. Good luck!