be careful with how you link it as well.
Lets say your site is
www.domain.com and you have a folder called "pdf" in a sub-directory in the main root so it would be
www.domain.com/pdf/
Theres several ways of linking. To save typing, I'll just show what goes in the href.
http://www.domain.com/pdf/file.pdf = This is not how you want it since you'll be switching TLDs (net to com). Also would produce security warnings due to http being explicitly defined, as said before.
pdf/file.pdf = If you're doing something from template files, this will
not work as it will search the folder the script is called from... Which in this case will be under skin1.
/pdf/file.pdf = This will start from web-root and go down. If you put a
/ at the very start of any link, it will start from your webroot folder. So this would properly go to the folder.
./pdf/file.pdf = This will be a mix between the previous two. It will start within the folder its called from and then go up one directory level and then search for the folder pdf. So in this case, it would go from skin1 -> root -> pdf
Just wanted to make sure you knew incase you were thinking of a way to automatically do this within tpl files.