Last dose of Clomid

That's right - I just had my last dose of Clomid for this cycle. Now we wait. On Friday, I go for my next round of blood work and sonogram. They'll let me know when to inject the Ovadrel either Friday or Monday, depending on the progress of the follicles. Which reminds me that I didn't mention what happened on my Day 2 appointment. The Doctor doing the sonogram paused mid ovary-whap, said "Hmmm." clicked the mouse to measure some black circle on the screen (ovarian cyst??) and proceeded to remove and wipe off the wand. He said they'd call if there was a problem, but otherwise I was to start the Clomid that night. Ok. I was trying to remember that, and he left me to dress. When I left the room, he was nowhere in sight to ask about this mysterious circle. I called the office once I got to my office, and asked "Ok, what was that?"
It was an Ovarian cyst, but because my hormone levels were fine, they weren't concerned about it. So I started the Clomid, and as I mentioned up there, I finished taking that already.
It's probably being back on Clomid that's making me feel a bit nutty, but I was all sorts of freaked out about the cyst. How will that affect this cycle? How do the "black pearls" that I have affect my ability to release an egg? Do the "black pearls" heal?
SO I have a lot of questions for my doctor, obviously, but if anyone out there is reading this and has gone through this - do you know the answers?