Congrats on your new girl! I personally think they can tell if you are uncomfortable. I have seen mine held by someone who was scared and he in turn was more on the alert. Once he was given back to me he calmed down. that also raises a question of "do they know who their "mommy" is??" but in any case, its totally normal for you and she to be skiddish in the begining but once she gets settled and you get used to her things should be alright i think.

Also, i have heard that its best to fee them in a different enclousure. But i have never done that and have had no problems. however, I feed frozen mice to my snake so he has never had to be on the hunt in any real way. He knows when the tongs come out that its feeding time and if he doesnt act quickly or strikes at the reflection of the mouse in the side of the tank (because sometimes i think hes not so bright) i'll just tap his nose with the mouse and he'll get it. The rest of the time he doesn't care if I am rearranging his branch or filling his water bowl or otherwise messing around in his tank. I think as long as you keep it uniform (always in the tank, or always out of the tank) she will become accustomed to whatever you are doing and will go along with it.

Good luck with your new girl!