Hi Lia,
The pain may be from the cyst but this is unlikely. One sure way of knowing is to go for that followup ultrasound and if the cyst is gone but the pain is still there ... you will have your answer. Even though a cyst is on the other side, we can experience what is called referred pain.
My own story may help you a little. I too used to experience pain around the pelvic area on one side (in my case, my left side) and in my lower back and inner left thigh. In September of 2007 I had an ultrasound done and they found an 8 cm simple cyst on my left ovary. I thought FOR SURE that my pain was caused by the cyst (as was my irregular bleeding .. another symptom). However, after performing a number of lower back exercises, beefing up the exercise (a walk everyday) and loosing 50 lbs, the pain went away. The cyst, on the other hand, is still there. My irregular bleeding has also been resolved by going off the birth control pill. If it is an external ultrasound that you are having done, try to go for this during your period as this is when it is less likely to show normal follicular cysts (most likely what you have).
In the meantime, perhaps you should investigate into the possibility of the pain coming from the lower back and extending around to your front lower right side. Kinesthesiologists are usually quite good at looking at posture and recommending exercises to help with lower back pain. I myself did not consult one. I found that rounding the back and "tucking in" your tail and then stretching this out for several times a day really helped. I also stretch my lower back by touching my toes. Just be sure that your overall posture is centered when you do this and that you are standing squarely with your legs slightly apart and your knees unlocked. You will want to consult a professional first to make sure that these exercises are right for you. A physiotherapist or kinesthesiologist would help. If it is a back issue, a nice professional massage will also do wonders so you may want to try this as well.
If you find that the pain persists, be sure to go back to your doctor so that further tests can be performed to find the source of the pain.
Best of luck to you.
Estria