After I've FTP'd my files and indexed them inot coppermine, can I delete the original FTP directory and files or is coppemine just pointing tho those files.
I guess the question is once mass uploaded, are the files in two places?
The files are not duplicated. Do not delete the files you batch upload.
Here's what you can remove:
http://coppermine.sourceforge.net/faq.php#minimumInstall