My go to person is Sage Goddess who is an authority on crystal use. So I asked her about it, and this is what she had to say-
Kelsie (Sage Goddess)
Jul 30, 2020, 4:42 PM PDT
Thank you for reaching out. You definitely do not have to keep them apart from each other. In fact, Athena has recently been telling the community about how she likes to display her smaller tumbled stones, natural stones, and some points in healing trays. She just piles them all in a tray! (I’ve attached a photo of an example) You can organize them however you would like, whether it be by the color, property, or just random, it’s completely up to you.
You can also keep your crystals in whatever room you would like to. There are certain crystals that would benefit different rooms better than others (such as keeping lepidolite and sodalite in a bedroom for peaceful sleep and black tourmaline in the room near your front door to help absorb negative energies before they enter your space), but you should put them wherever they feel right for you.
It’s true that crystals can and do absorb both positive and negative energies from people, but this can happen whether the person is touching the crystal or not. Crystals can absorb the energy just by being in the same space as the person giving off the negative energy. You can fix this by just regularly clearing/cleansing your crystals and your space, especially before you use them for your energy work. I’ve attached another photo of different ways you can cleanse your crystals. If you do like using sage, here is a blog with different tips on how to use sage to cleanse: https://www.sagegoddess.com/smudging/sage-goddess-smudging-protocol-for-clearing-sacred-space/.
Athena often also talks about how there is no “right” way to do crystal healing. You can store and use your crystals however you are called
I hope this helps. Please let me know if you have any other questions.
Love and light,
I also know that you do not want to mix rough stones with tumbles as they can scratch them.