If she's pooping round worms, she has an overload of worms and won't feel right until treated. You can treat for roundworms and still give the antibiotic. I'd continue the antibiotic for 10 days (if that's the normal recommendation) and then if not 100% by then, switch to baytril. It's my understanding that baytril is a stronger antibiotic.
But, you don't want to go back and forth on dosing. If the recommendation for amoxicilin is 7-10days, then after day 7 you could switch. Her gut is going to need probiotics. Just give a couple hours apart.