How do you intend to access these files in the future? That would affect the best way to store them.
For example if it is Windows, then you would want a Windows compatible file system format, such as "exFAT". If another Mac, then the Mac native file system format would be best.
Once you have that decided, you can create a directory structure on the external disk, such as Mac1, Mac2, Mac3, .... Then drag and drop the folders of interest to the respective folders associated with the Mac the data is coming from.
Also, I would strongly suggest 2 things.
A) use multiple external disks with redundant copies of the data, as you do not want to trust the data to just one device.
B) I would try to keep one of the disks in service, as magnetic data tends to drift if left idle. In fact I would make a new copy of the disk every year or so, just to make sure the magnetic fields are refreshed (disk cloning software can do this easily enough; for Mac I would use Carbon Copy Cloner or SuperDuper; for Windows, I do not know what is the best offering, but it does exist).
You might even consider also paying for an on-line backup service, such as Dropbox so that you also have a professional service keeping a copy refreshed (BUT DO NOT put 100% trust in an on-line service, as business make mistakes or go out of business, so you want your own copies too).