I used to raise exotic birds in a former life, and when handling birds you always remember to let them keep their feet on a perch. A stick or hammer handle or arm, anything will do. If they are not perched, they are stressed and fearful, so keeping them on a perch of any kind will help keep them calmer as you handle them.
I figure it's same with queens, they want their feet on comb. So, I grab her with my writing hand by the wings, then as I'm setting her on the comb, my other hand comes in to gently grab her along the sides of thorax, holding her with her feet on the comb. I then have my writing hand free and I dot her with a pen. I then put her into a roller cage to dry off before letting her back free on the comb.
I've found that the queens, as you are trying to mark them, are leaning their heads way back to try to prevent you marking them. It is at that moment to be very careful or you, at least I have, will dot their eyes and/or antenna. They really do resist being marked, and the workers try to clean her off immediately. The way they act, it's like it must really be a bad thing for the queens, they really hate it. (And just wait till one time she faints on you after you mark her and start to put her back into the hive. It really made me wonder, the time or two that has happened.) But, I mark my queens anyway. I like to know if they replace her, and it does make it faster finding her when needed.