That being said, the best organization tip I can give you, I learned from my brother-in-law. My sister told me how he organizes everything he needs for his trip into a folder and puts them in the order of when he'll need them. For example, the first page will probably be the itinerary or first flight out. Followed by rental car reservations, hotel reservations, or whatever will come next. I tried this out a few years ago and found it to be very easy and useful! I was able to locate the documents I needed quickly and didn't have to keep taking them out of my bag and risk misplacing them. They always stayed in my folder (with clear sheet protectors) and it was easy to find.
I also include in my folder other information that will be useful on the trip so that I don't have to search for it on the internet. For example, on my upcoming trip to Tokyo, we know we want to visit Tokyo Disneyland and Puroland. Since these are theme parks and have seasonal hours, I looked up their hours of operation schedule for the week that we'd be there to determine the best days to visit. We've been to Disneyland before and know that weekends are busy, so plan on going there during the week. Also found a coupon for Puroland that I printed and will bring with me.
Another tool I got was a map of Ginza. My friend Susan, who frequently visits Japan gave me the map to explain to me where the Kabuki-za is in Ginza, along with the Sanrio store. I decided to take the map with me so I could reference it before we head to Ginza.
You can find one of these types of folders at Longs here in Hawaii. I have a couple of them in case I'm planning two trips at once.
Before I knew how to use google maps, I used to also print up the driving directions ahead of time. But now I found that using my google maps on my phone is better than having to look at a physical map because it won't distract me from the road.
We also look for helpful apps to download on our phones prior to the trip. My husband found a Tokyo Metro app that contains the subway/train maps that we'll have access to whenever we need them.
I found that this is the best system that works for me because it is simple and easy to use. Hope that helps you in your trip planning!