WordPress does some "special" things with files uploaded through their upload process so that your website frontend can perform optimally. While it is possible to upload files from FTP directly into your WordPress structure it is not something I would advise IF your goal is to use them in your WordPress website with fer exceptions.
If you are stuck on uploading files without using WordPress you just FTP them the same as you would with any other session. The particular directory you want to upload to depends:
Of course your directories will contain more information, files, themes or whatever. As a general rule I don't upload any files to the wp-content/uploads directory as that is the WordPress default upload path. I try to put any theme/template files directly into the associated theme directory. FTP programs like FileZilla, Fugu, Cyberduck and gFTP are great to provide a look into the FTP structure of your website WordPress or otherwise and easily transfer files in and out. I hope that helps?
...turns out that my two cents is worth less or more depending on the current exchange rate.
roy darling *my posts seem a lot shorter in my head