With allergies, children usually have a runny nose that does not seem to wax and wane, as a cold does. The runny nose is more constant, with thin clear drainage. Children may have frequent sneezing as well. Some children with allergies will not have a runny nose, however, and may just have nasal stuffiness.
Asthma can be related to allergies, and while children typically wheeze as the manifestation of their asthma, some kids will only cough. If the symptoms of cough only occur with exercise, that is another warning sign that there may be some asthma. Coughing that is more prominent at night is also suggestive of asthma. The other thing to remember is that asthma is also a familial disease. If one parent or sibling in a family has asthma, eczema, or hayfever, then that child is more likely to have asthma.
If your child's symptoms do not seem to resolve completely between episodes, then I would be concerned that there is more than a cold. Talk with your child's doctor if this is true or you feel that she has signs of allergies or asthma, as effective treatments and preventive measures are readily available.