I am trying to train custom object classifier in Darknet YOLO v2 https://pjreddie.com/darknet/yolo/
I gathered a dataset for images most of them are 6000 x 4000 px and s
You don't have to resize it, because Darknet will do it instead of you!
It means you really don't need to do that and you can use different image sizes during your training. What you posted above is just network configuration. There should be full network definition as well. And the height and the width tell you what's the network resolution. And it also keeps aspect ratio, check e.g this.