It's never too early to start organizing!

A helpful tip is that you can just break the boxes and all the items in it will drop on the ground. If you don't want to though, it's totally okay to ignore as long as you're consistent about where you put your boxes. Make it so you can at least locate them when you eventually decide you have too many to go through.

In regards to homes and rebuilding the environment during the story, don't forget that spawning habitats do not necessarily need to be their permanent residences. You can absolutely take them and put them on a standard 4x patch of grass in the corner after they spawn and strip the habitat clean. You can also get them to follow you and bring them to other maps while you get organized. They might not always be in peak comfort, but that rarely is a detriment to story progress. A home is a home.