Batch Upload Files
If you wish to upload many files at once to one location on Moodle you can put them together in a "batch" or archive. In Mac select all the files, right click on your mouse, and click on "Compress". On a PC select all the files, right click on your mouse, hit "Send To" and then click "Compressed Zip".
Back in Moodle click on "Files" in the lower left of the Administration block. Navigate to the folder you wish to save the files in. Click the "Upload a File" button and upload the zip file you created. Zip files will appear on the Moodle folder with an "unzip" command. Click unzip and Moodle will show you the name of all the files. Click OK and you will return to the folder view, where all the files have been unzipped and are visible.
When you unzip a folder it maintains any directory hierarchy within that folder. In other words if you zipped a folder that had sub-folders those would still be there when you unzipped it. Therefore if you want to organize your files the easiest thing to do would be to set up your folders the way you like them on your computer, then make a zip archive of the folder and upload it.