When my Dr. put me on clomid the first thing she said was that she had to make sure that I didn't have a cyst first because Clomid can increase the size of the cyst and make it worse.
If your Dr. is monitoring you with U/S though throughout, I wouldn't worry to much, especially since they are already aware of your preexisting cyst.
My Dr. didn't even do an U/S first, all I got was an internal and she somehow knew from that that I didn't have a cyst. I'm not convince though because I always get a dull aching pain, especially on my right side, occasionally on my left, and the first cycle of clomid didn't work. I'm assuming because I'm not pregnant and I didn't get my period, so frustrating!
I have been on clomid off and on for the past 5 years. We just went back to the fertility specialist after a break and this was the first time they monitored me for cysts before I started taking the clomid. I had to go on the second day of my period and they did an ultrasound to make sure that I didn't have a cyst and then they told me to go ahead and take the clomid. In the past, I was never monitored for a cyst, so maybe it is something new that they are doing with clomid. You could ask if they will do an ultrasound before you start taking the clomid.