I tend to wrap loose tubes or tube pairs in bubble wrap or paper and then put them either in ziplock bags with gaffing tape for labeling or in a small box and seal the bubble wrapped tube pair with a gaffing tape label.

Most tubes come in branded and labeled boxes already and you can also store them in there and stack em in another larger box, add some crumple loose paper or wrap the tubes in their boxes in bubble wrap if you want to extend the life of the original boxes. Store in a larger box. That's what I did anyway. I ended up settling on a really good end game for me pairing and haven't really tube rolled since, and I bought ALOT of tubes that I maybe shouldnt have for my Little Dot MK2... oops.

What tube amp are you currently tube rolling on?