Ryan Cramer details some of the problems with select/multiple and a few good alternatives. It’s useful in certain circumstances, but unintuitive and error-prone. Instead, you can create a list of checkboxes inside an element with overflow:auto set, or use a jQuery plugin he developed.
ISINC has a writeup on how to pass a batch file of commands to Window’s command line FTP client. You can then create a Scheduled Task to automate them.