"Do you have a stomach ache?"

Not in this case. When there's a є, it has to be followed by a noun and it means you have something (literally, there is something with you). У somebody є something = Somebody has something (literally something is with somebody).

Болить means hurts, since it's a verb it won't be used with є, the constructions are different. У somebody болить body part = Somebody's body part hurts (literally, body part hurts with somebody).

Mixing them up would be like saying Does your stomach is hurts? or Do you have hurts your stomach?