the method you have described is valid , and technically you can use it without a problem.
Other options you have are :
1.Upload via FTP to a “PDF” folder (or whatever name) and MANUALLY link the files.
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Change the default “upload” folder only for the time you upload the pdf files (this method is not reccomanded and will work only on a more “static” site where pdf´s are uploaded only once or twice in bulk)
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as for plugin – there is this one
http://wordpress.org/extend/plugins/wp-easy-uploader/screenshots/
which is a bit old but might help you. (I did not verify if works on current release) -
write a custom function that will either A: change the upload dir ONLY for PDF (easy to write) or B: Let you choose plugin folder for EACH upload.
Right now I am a bit pressed with time, but if you are interested in option 4 let me know .