Some of mine are in boxes, some out on display, some in little bags, some I carry on my person constantly, some are gridding my house out - I don't honestly think it matters.

The only things I would suggest is if you are carrying stones with you to carry them in seperate bags or pockets - just because a sharp piece of Quartz can scratch and damage softer crystals like Fluorite.

Energetically I normally store my clear quartz on its own and the moldavite on its own, just so I'm not overpowering my other crystals. As for clashing energys, you'll see if a stone isn't happy somewhere cause it will loose its sparkle.