For the cruise docs, I just used the box that they came in. Put it into my carry on bag to the terminal. Once you check in at the terminal, you don't need to carry your cruise docs with you anywhere (of course you don't want to throw them away). During the cruise I kept them in the room safe (all rooms have a lockable safe).
I had a passport satchel with neck lanyard from traveling for business. I put all 5 of our passports in it along with credit cards, driver's licenses, etc. For leaving the ship, I used this. I stuck our ship ID cards in this along with the passports.
All you need to carry with you around the ship is your ID card that you get during check in at the terminal. Many people bring or buy onboard (we did) a card holder with a neck lanyard, or just put it in your pocket.
I also had a manilla folder for storing Daily Navigators, ship excursion receipts, etc. This basically just stayed in the room as a single point of storage for my papers.