ruptured cyst? please help

I am 6 weeks pregnant today  and yesterday I experienced SEVERE cramping on the right side only with nausea and vomiting. It started around 8 am and peaked around 11 when my husband came home to find me sobbing in our bed. At this time I was not bleeding but the pain was very intense (I labored for 36 hours with my 1st so Momma ain't no wimp! ) 

We called the dr and went to the ER.  They ruled out appendicitis since the pain had started to go away. When I went to pee in a cup

I realized I was bleeding. It was mostly brown mucousy discharge tinged with blood. 

I was given an ultrasound but it was determined that it was too early to see a fetus. My blood HCG was 623. 

(Has to be 1,000+ to view on ultrasound). They gave me a Rhogam shot since I'm A-, and said "follow up with your OB, we don't know what happened. Could be ectopic, could be a miscarriage, could be a cyst." My ultrasound did show free fluid in the abdomen. And I had stopped bleeding/brown discharge by the time I got home. When I miscarried 2 years ago (at 6 weeks) I bled for days and felt very sick and horrible the whole time. I feel fine now, just slightly nauseous, and my right lower side is a bit tender. 

I am supposed to have blood drawn tomorrow and have my HCG levels compared to make sure they are increasing. 

I believe I had a cyst that ruptured, the discharge is from the cyst, and I am still pregnant. 

Has this happened to anyone else? Pregnant or not? How did you find out it was a cyst?