You've been scanning away. Time to organize. If you follow the outlines of this flexible system you will always be able to find your digital documents. Pictures are a separate topic.
I use an external hard plugged into a USB port for my genealogy. It keeps my genealogy all in one place, can be easily removed and taken with me if needed and - this is important - it gets automatically backed up with my offsite backup procedure. It also makes it easier to create your own filing system because you don't have to fight with your operating system's idea of where things should be filed.
Name your people files in the following manner: birth surname, first name, type date location. An example: Downing William census 1860 Chester.pdf. I suggest you stick to surname then first name. If you want a different order for the other information that's fine. There is no right or wrong. You are the one who has to find the documents later. Just be consistent.
The key, at least in my experience, is to be consistent. Consistency trumps just about everything. If you use a numbering system the number should be the first word in the file name. I don't use a numbering system. It's just one more thing to organize and remember but if a numbering system works for you do it.
Make eight directories, one for each birth surname of your great grandparents. Keep in mind that if you are doing this for your children that would 16 directories. Put everything pertaining to that ancestor in that folder. If you have a lot of information on ancestors prior to your great grandparents you may chose to make a separate directory for additional surnames. It doesn't matter how many directories you make. This is digital. You have the room. Do what works for you.
I hear you. What about great grandmother Jane who was born a Smith and married a Jones? Put her in Smith. If you want to put a copy in Jones go for it. It's digital. Duplicates aren't an issue.
Also make directories for cemeteries, census, birth, marriage, death, land, etc. If you collect funeral cards make one for those. My census file has subdirectories for each federal census. A copy of all census documents I have is in that directory. Another copy of the individual page is in the appropriate surname directory. For documents in these files the name might be 1880 Census Illinois Logan Laenna.pdf. Illinois is obviously the state, Logan is the county and Laenna is the township. Using spaces between words makes it easier to find them through a digital search if needed.
Get the idea?
Now go to http://www.voidtools.com/ and download the free Search Everything. If you goofed in spelling but you included all the elements you can search on any one of the elements and find the file.If you misfiled it you can still find it. Search Everything only searches files on your computer, including the drives attached by USB. It will not search network attached storage or home servers.