I don't know how effective the medication is, but I know you'll probably have to keep taking it unless you have part of your thyroid removed either through radioactive iodine treatment or surgery. Yes, frequent and loose bowel movements are common with hyperthyroidism and should resolve with treatment.
I would suggest doing some research into the topic, especially considering radioactive iodine treatment (which is not as bad as it sounds) or surgery. You'll want to be fully informed on your condition and have questions ready for the doctor. This is important, so make sure your doctor explains everything to your satisfaction.
Good luck.