I had signs of a uti but my doctor said that my test was neg. for it but gave me antibiotics anyway.. everything cleared up but now i'm feel ill ?

Likely unrelated: Sometimes cystitis is missed on a urinalysis, you really need a culture. Treating empirically(without urinalysis) can sometimes improve symptons and the culture returns unremarkable. Being "i'll" is kind of vague but not likely related to the urinary tract and most short courses of antibiotics will not mess up the bacteria in your colon; you could try probiotics if it's colon but should pass.