Got some more info from the vet's office...

The 1st time they analyzed her urine they found struvite crystals, the most common seen crystals, and can lead to bladder stones. This time they saw no crystals, however there was an increase in the number blood cells, both white and red. The white indicates a lingering infection, which is why they are trying a stronger, more brad spectrum (fights more types of infections/bacteria's) then previously. The RBC's do not mean she is loosing blood, but 1) that blood is being sent to the area to help fight infections and 2)that there is an irritation or inflammation. She is not "bleeding" as if she was cut, but it is more a presence of blood on cellular level.
They felt that from what they were seeing if a fairly common infection, treatable with the medications. They like to give it a few weeks for the meds and the diet adjustment to work before they go to more extensive, expensive measures. They feel two weeks is a long enough time to see some of this (and they have seen improvement), but not enough to delay treatment, although nothing they have seen indicates a more serious issue, then the crystals, which have been eliminated with the change in diet and the meds, or the infection now, that they new antibiotic should take care of. If, in 2 weeks there is still a problem, that is when they would think it appropriate to start looking at ultrasound/X-rays, more extensive blood test, etc. depending on what that analysis looks like.