My daughter has yellow gook in her eyes and they are also watery. She does have allergies which she takes Flonase and an inhaler for! Is the yellow discharge caused by allergies as welll? And if so what can I give her?

Antihistamine. Although discharge from allergies is usually clear/watery, there can be some yellow/thicker appearance to it. Both eyes is more suggestive of allergy than infection. Consider over the counter antihistamine like zyrtec or Claritin (loratadine) for children. If it worsens, or the lids are matted together then an antibiotic drop may be needed. If the allergies cont. To bother, antihistamine drops can be rx'd.
Allergies. Based on your description, it is likelydue to allergies. Trycool compresses, chilled artificial tears, and topical and/or oral allergy meds.