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.
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!