I keep all my boxes broken down right now, and then I box up those broken down boxes in other boxes to store in the garage or a spare closet. It still takes up a ton of space. My collector mentality says "But they are worth something!"
The rational part of me that says, "You will never sell them" is starting to win. I know if I toss them all I will feel bad for a month or two, but then will get over it. Maybe in a month or two I will finally snap and toss them all out.
As for instructions, I know that BentBricks said he rarely keeps them and does PDFs, but I just have a hard time telling colors on the PDFs. And I have a few filing cabinets for the instructions. Those I feel I should keep, because i never know when I will want to rebuild something old.
Still on the fence about boxes. Hell, about to put some UCS sets that have been broken down for almost two years into the collective since I don't have enough display space for everything.
Oh, how this hobby evolves as you get more stuff from it.
any large sets I keep the boxes for. Flattened down they still take a lot of space but I'm resisting throwing them out in case I want to sell a few later on - I cleared out my modulars mainly for lack of space and the box+instructions is really needed to keep the value up.
I do use the printed instructions but usually handle gently and store in a box afterwards - I find PDFs not ideal for a relaxing build. But I keep the instruction cardboard backing and if I sell, a quick wrap with cling film and then a hair dryer to shrink wrap it is a pretty good way to get them back to near as-new presentation wise