Petunia sounds like such a little sweet pea! I’m so glad you’re settling in together and it sounds like things are going really well.
From my experience, I found that most rabbits love to explore but it can be helpful to start small and expand their space over time. This not only helps them get used to a new surrounding a little bit at a time but prevents overwhelming their senses (and possibly help with littler training if you don’t want them to stray too far from their box). I use an x-pen to close off a small area and let me rabbit explore. Every few days, I make the pen a little bigger. Once you exceed the size of the pen in a square shape, you can then use it as a fence to block off half a room, etc. as their space grows.
Starting small helps the bunny learn the scent of a new space and can often keep them from marking too much. She seems young so it might take a while (and she may revert backwards once in a while) but I think you’re on the right track as long as everyone is separate until they can be fixed and have time for those hormones to settle. Good luck!