In most asterisk server deployments, Polycom phones are provisioned via files that are located in the /tftpboot directory of your server. Every time you reboot a given phone it will pull down its configuration files. So to make changes to a phone, or a group of phones, you would simple make edits to the files (they are plain text files) and reboot the phone. The Polycom directory configuration files use the following naming convention: macaddress-directory.xml (it is a regular xml based file).
For example, if your phone has a MAC address of 0004f215e63c. It's directory configuration file is called:
You would simply need to download this file to your computer, make the edits, and then re-upload it to the pbx, overwriting the old file. Then reboot your phone to effect the change.
Most linux servers run a "SecureFTP" daemon process which communicates via the SSH protocol (port 22). This replaces the old standard insecure FTP protocol. Most modern day Windows FTP client software programs can communicate over the SSH protocol (including WSFTP Pro).
You can find a detailed explanation of the format of the mac-directory.xml file in the Polycom SIP 2.0 Administrators guide (you can download this on our support site).