you just have to keep looking. most of the time unless I have a specific reason to find the queen if I find brood with eggs I quit looking. It helps to have marked queens.
I agree with rober. Eggs and larvae will tell you how long ago she was on that frame. Those that keep looking for the queen can run this risk of chilling or drying out brood, promote robbing, and end up with cranky bees.
If you need to find the queen for other reasons, like requeening, you can place a queen excluder in between the two brood boxes. In a few days look for new eggs and larvae. When you find new eggs and larvae you will know which box she is in. At least then you will have reduced the search by half.
Others may have some suggestions too.