Anyone have any suggestion for a less stressful/easier method of putting the medicine on them, what method do you use?
From my wife the veterinarian:
In general, the more you try to pin down a cat, the more they'll struggle. So, the less force that can be used, the better. Are your cats not big on touch in general, or are they pretty physically friendly most of the time, and this is the only time they run?
If they can smell it open beforehand, get a co-conspirator to help you. You get the cat settled in with you, and they open the tube and hand it to you.
Can you try to get them while they are asleep?