Chances are they will be okay, but it's painful to watch, isn't it?
You don't mention her pulling fur for the nest. Sometimes first-timers don't do this and it puts the kits at risk from chilling. You can encourage her to pull fur by gently plucking some from her tummy and dewlap. If that doesn't help, you can used teased cotton balls or batting, dryer lint or feathers from a pillow to give them something soft and warm. Hay, straw or wood shavings (not red cedar) would be better choices than fresh grass for nesting materials--warmer and more absorbent.
If she doesn't settle down and keeps stepping on the kits, you may want to consider removing the box of kits and just giving it to her morning and evening so she can nurse them, at least until she calms down. Most does don't feed their kits more than twice a day anyway. Be sure to keep the box somewhere safe, away from other animals.
Your doe may just be a little nervous--first-time momma jitters--and you may be making it worse if you are checking on her frequently. Short of removing the box, there really isn't any way I can think of to change the doe's behaviour. She may quit on her own once she is used to being a momma.