You could have a secondary cpbackup.conf file with the FTP details in it. ONce you have that, create a shell script that:
1. Renames the real cpbackup conf file
2. Puts the FTP cpbackup conf file in place
3. Executes /scritps/cpbackup --force (without --force the backup might fail with 'Backup is already up to date').
4. Once the backups complete (will have to monitor processes for this), undo steps 2 and 1
You could then execute the shell script manually.