I make nearly all my food for DH and me from scratch as well. And I just measure everything (well, not really everything, I don't measure spices and vinegar

) before adding it to the pot or pan and write it down on a little block of paper I keep in the kitchen. And then, either while the food is cooking or sometimes later, I go to the page where I record my calories (I'm using a German one because it has all the food I buy here; I think fitday.com is a US one) and put everything I put in my food in (well, only half of it, because the other half gets eaten by DH *lol*).
It just tells me the calories for all food there is, no matter if pre-packaged or not.
Did that make it any clearer for you?