As much as I hate to do it...I scruff the ones who won't cooperate. My vet asked one time how I gave them medicine and I explained the towel and the fights we had. He told me that all I did was traumatize the cat by making it such a big event. He said scruff their neck, twist their head slightly sideways, then pop in the medicine. It's not as simple as it sounds and it a takes some practice but I do find that it was better for me in the end. It is over in seconds with most cats. I still have a couple that require the U.S. Army to get a pill down them!
So my advice is to try different methods and the one that is the fastest and easiest for you and your cat is the way to go. GOOD LUCK!!!