The general goal is to reduce risks for further kidney deterioration. Some of these risks would be the presence of hypertension or diabetes. Obesity may be related to diabetes and may then be indirectly related.
It would then be a good idea to obtain an estimate of kidney function and to confirm whether the cyst is single or multiple. This would help establish how urgent is the need to control any of these risk factors. Confirming the cause of the disease would also be important, to make sure it isn't something more serious like kidney cancer.
If the pain is significant, it may be important to discuss the possibility of removing the cyst if pain medications would not be able to control the pain. Bear in mind that some pain medications may also damage the kidney in the long term – so again, here is another point to discuss with your doctor.