Over many years, I've seen that family historians fall into at least one of two camps, but sometimes both. In the first camp are those who use 3-ring binders to organize all their family history notes and documents. In the second camp are those who use folders. Then there are people like me who use a combination of both, sometimes duplicating items intentionally.
Which ever method you choose is fine, as long as you do something to keep your ever growing collection of content organized. One benefit to using folders (meaning physical folders) is that you can replicate your folder system online as well. Use Surname, Placename, and other folders on your computer desktop, as well as in your email client, and also to keep your web browser 'Favorites' or 'Bookmarks' organized.
Don't forget too that you can nest folders inside one another just like in your physical file drawers. This can help you keep like groups together.
There are many benefits to this type of online foldering system and it's never too late to start. You can always create folders and gradually move files to where they belong. If you're not sure how to start, simply create a folder named GENEALOGY or FAMILY HISTORY and gradually move all your related files and documents into that main folder. Then you may wish to create Sub-Folders, perhaps one for your paternal line and another for your maternal line. Gradually move files into one of those two folders. Continue creating sub-folders and moving files until you can quickly locate and save your documents and files. You'll find this takes time to set up, but will save you a LOT of time in the long run.