If I get a urine test to see if I have ureaplasma while im currently taking amoxicillan, will th amoxicillan cause it to be negative even if I have it?

Maybe, but why? Probably there is no point in being tested for ureaplasma, unless maybe if you are under the care of an STD specialist. Ureaplasma is present in up to half of all people, so your test is likely to be positive, but usually it is harmless. If you have symptoms, a positive test would not mean Ureaplasma is the cause. Amoxicillin probably would not make the test falsely negative, but it is possible.