I skipped my period. So I took 2 hpts, both negative. Then shortly after got my period but, it was longer and darker than usual. Now my pee is cloudy?

Likely Unrelated. These symptoms seem to be unrelated. Being late for a period with a negative pregnancy test is most often due to stress causing fluctuations in hormonal levels or anovulatory cycles. Cloudy urine can be a symptom of a urinary tract infection and should be evaluated by a physician.
Possibly unrelated. Menstrual irregularities are v. Common. Cloudy urine could be due to a UTI +/or small amount of blood in urine or just plain normal urinary sediment. Worth checking with a urinalysis.