Well, by weighing and logging everything. You are correct that it takes a lot longer when you do that. That's the cost of keeping track of your caloric intake. I also do not account for any nutrient loss or divergence from different cooking times, leftovers, or from different species.

I only weigh everything I eat when I am actively trying to lose weight, however, and when I am doing so I deliberately restrict my diet to meals where I won't waste a lot of time weighing everything. If I'm trying to maintain or gain weight, I don't really bother with it.