Does resizing images during training affect the bounding box annotations?
My doubt is whether the resize would now change the position of my object according to annotation?


Yes, it will.


  should i annotate on the resized images(resize them myslef before
  training?)


No, you should annotate at the original size.

You solve this by applying the corresponding transformations on your bounding boxas well. So if you resize your image, you rescale your bounding box. This allows you to expand to different image augmentations without redoing annotations for all of them. 

I recommend you to chose a library that has to ability to apply transformations on both images and their bounding boxes. I use albumentations but there are others such as imaug.