Having gone through a dozen or so computers and three decades of software updates, we've found it a good practice to IMMEDIATELY, when unpacking a new one, use a small box to put ALL OF THE PROGRAM DISKS, Manuals, registrations, etc for the new machine IN ONE PLACE.
We've used the small plastic "shoe boxes" you can find at places like WalWart, Hobby Lobby, etc. (About $1 each when we got our first bunch, but probably $4 each now?)
The boxes that purchased software comes in are made for display in the store, not for storage at home or at the office. In some cases you may need to clip off a "Registration" or "Certificate" or "Key Code" and put the original piece of the box panel with the disk(s); but the average 3 cubic inches of content usually is in 3,267 cubic inches of box, which makes for rather inefficient use of space.
While it must be recognized that nobody reads the manual, it is strongly recommended that you keep any user manual that comes with the computer. It probably looks pretty useless when the machine is new, but may be the only place to find which two points to short circuit on the motherboard to dump the BIOS when you forget a system password, or to find the specific specification for the chips you need if you decide to upgrade memory, ... or other trivia of the kind.
Manuals that come with software often are useless but be careful about discarding one you might need later. Some wise evaluation may be required in the interests of space availability. Program disks generally should go in the box for the machine on which the program is (first) installed.
Since at one time we were a thriving small business, Lin got busy and "organized" our supplies and we have a single shelf with 48 of the (nearly) identical shoeboxes. Each computer has its own box, with the rest of them devoted to "supplies."
As the business is less active now, anyone who wants a shoe box full of "brand-new" ballpoint pens filled with dried up ink, or a few hundred Post-It® stickers with dessicated adhesive that won't stick to anything, or some of the few thousand staples that fit only the broken stapler, please PM her - not me.
If you do choose to put everything in one box, even if you only have ONE BOX, do put a good, visible label on the box.
And NEVER put a "rubber band" (elastic) in any box that contains ANYTHING you might want later.