It sounds like you have a good vet--he/she started your kitty on a nice moderately low dose (which is good because it helps avoid tummy upset) and twice per day (which is good because the medicine has a pretty short half-life and needs to be given at least twice per day to keep the levels more even). The bloodwork after two weeks is important because you'll be able to determine whether the amount of the medicine is working or whether the dose will need to be increased or decreased. The renal panel will allow you to see how the kidneys are doing. Sometimes the kidney values increase after the cat's thyroid levels normalize--this is because the high thyroid levels can hide existing kidney problems. Hopefully you won't have to worry about this.
Once you find out how CC's body will tolerate the medication, you can consider whether radioiodine/I-131 would be the right treatment option for you and her. In many cases, treatment with radioiodine can destroy the cells that are causing the excess amount of thyroid hormone. This can mean no more pills or in rare cases supplementation with thyroid hormone (which is much easier to manage than treatment with methimazole). The treatment has a very high success rate--it is expensive, however, due to the regulations surrounding radioactive material and its handling.
For now, just focus on getting the pills into your kitty. I found that buying some small gelcaps was helpful because the pills are very bitter. If she's hard to pill, you can ask your vet about compounding the medication into a liquid or a transdermal gel. Make sure she keeps eating her meals--if her appetite wanes you can ask the vet about appetite stimulants. Good luck and keep us posted.