I did a cut out earlier in the year I messed up and had to trash most of the brood. I started her off with about 1/3 of a deep frame of brood. Well when I released her from the queen catch clip they immediately swarmed. Then I caught the swarm and stuck a frame of brood. They started building up spreading to 3 frames. Then we had a wicked rain/hail/wind storm and the hive fell over I lost 2/3rds of a frame of new wax and brood. I righted and tightened down. Well she survived but I thought I should mark her. I'm an idiot because instead of marking the thorax I marked her head too. I thought she was a goner. I put her in the hive and the girls must have cleaned her up. It's been 9 days and she is still laying and no supercedure cells. I can't believe how tough this queen is. (http://img.tapatalk.com/d/14/05/21/vyta8u8y.jpg)
...why that's a pretty green :lau: Looks like you ran her through a carwash. :-D
I have all the stuff but I've never marked a queen. I want my eyes trained to see her without any help. That being said, I understand it's best to take the marker and mark some other things before you mark the queen. It's said that some markers will dispense a lot of color with the first marking of the day. Others have said what you have saw - the bees will clean it up. Good luck.
A commercial beekeeper let me watch him mark queens a few weeks ago and it gave me the courage to try. I had her, I aimed for the thorax then marked the wings. I tried again got her down then I aim for thorax and again I twitched and marked her head then back. She curled up and in my shock I dropped her on the ground. I quickly picked her up and put her in the hive and prayed. I practiced on like five drones with no problem.