FTP Backup script through VPN tunnel.

Hello all!

First of all, i'm a total rookie with networking, so excuse me if this is a particularly stupid question.

I've run a script through SSH with Putty for a scheduled backup of the fortigate 60e. 

config system auto-script
edit "backup ftp"
set interval <minute>
set repeat 0
set start auto
set script "execute backup config ftp backup.conf <IP> <username> <Password>"
next
end

The FTP server is working fine but this script has to go through the VPN tunnel which is configured on internal port 6 instead of using the WAN port directly. 

Do any of you know how to script this? 

Thanks in advance,

Thijs