but it is difficult to manage everything in Finder
Don't move the image files using the Finder - this will break the connection between image versions and original files.
Select the images in Aperture's Browser and use the command "File > Relocate Originals" to move the original image versions to the folders where you want them.
Do not manage them in Finder. Once you import a file into an Aperture Library, you must use Aperture and only Aperture for almost all file management. (On import, your files become, to Aperture, "Originals".)
Aperture has robust tools for managing Originals.
Decide how you would like your Referenced Originals organized, then use "File➞Relocate Originals" to gather your Originals and re-file them.
Note that the Finder folder structure is strictly a convenience for you. Aperture does not care, and will do equally well with all your Originals held in one Finder folder (though, at the least, you might use one Finder folder for each year).
Instructions for relocating your Originals are on this page in the User Manual. ("Master" is the same as "Original". Apple renamed them.)