For serving size, I usually put it next to the name of the food. For example, when I do homemade marinara sauce, I put in the title box, Marinara Sauce (1/2 C.). Then I just leave the quantity as one when I enter it into my log (or do .5, or 1.5, or 2, or whatever, depending on how much I ate). I'm not sure if this answers why the calories were changing for yours, though. Just be sure to always click the box instead of enter...the enter key does not always save things on this site.
And now that you don't have to be perfect, you can be good.