I'm not sure why you got the negative result maybe the urine concentration was too weak? was the bleed just a small amount? Not like a normal period type bleed. Bleeding in pregnancy is quite common and as long as it wasn't very heavy with clots then you should be ok. If you have had a positive pregnancy test since and are gaining weight as you would expect by this point then at a guess I would say yes you are still pregnant.
Have you had an ultrasound yet or scheduled to have one soon?
I would call your physician. Make an appointment for another ultrasound. They may need to draw blood for a quantitative HCG level (pregnancy hormone). From these tests your physician should be able to tell you.