If the PHP interpreter is installed as a shared object, it runs within the web server process. Typically, web servers (should) run with very limited permissions, for obvious security reasons. If this is the case, you can change the ownership of the directory you're uploading the files to the web server user, typically 'nobody' or 'wwwrun' on *nix systems. But you'll need to be 'root' in order to do this...
Alternatively, you could create a directory outside of the web servers ~/htdocs path which is owned by the server, and then create a sym-link to that directory in your ~/htdocs path; while this offers some protection, some web servers do not follow sym-links.
Best bet, use ftp to upload files, since there are some security considerations when using PHP to upload files. The upload capabilities of PHP are convenient, but I always disable that feature for these very reasons.
Good luck...