Tor only works directly as a SOCKS proxy. There are a couple options here - first is the 'torify' program (which uses tricks to force all sockets in a process to be sent through Tor even without application support for SOCKS). That'd be the simplest solution, probably. You could also set up a HTTP proxy to redirect to tor (this is what privoxy usually does - although it'd need to support non-HTTP connections, which i'm not sure it does), or simply use different software that includes SOCKS support :P
I don't think this is relevant in this situation, but always remember that passwords sent in plaintext over tor are visible to the exit node. FTP would fall under that category.
- John