How do I fill in around waste pipes?
Can you just fill it with sand and level it? Yes, I suppose so, though it is not a good idea. This would probably be viewed as a problem when you decide to sell this house. It would be a tripping point, so dangerous. It might also be an avenue for radon gas to get into your basement.

Do you need to have rebar into the sides? I doubt that. There is no load being carried here. No real need for serious strength.

Just pick up a few bags of cement from the home store, mix it up as indicated in a wheelbarrow, and trowel it in. Make it reasonably flat, but you need not be a perfectionist if this is simply a storage area. Just try to minimize any trip points.