Let me try to explain it better:

If your NICs are connected to 2 different subnets and the server you are ftp'ing your data to is in the same subnet as the secondary NIC, you probably don't need to do anything. And I say probably, because I don't have specifics, i.e., don't know if the secondary NIC was properly routed from the get-go. Quickly looking at the output of netstat -rn will tell you

If your secondary NIC is NOT in the same subnet as the server you are ftp'g to, or both NICs are on the same subnet, then you need to use the route command to tell your box that all traffic to <ip you are ftp'g to> has to go through gateway <ip of your second NIC> , NOT THE DEFAULT gateway. You would be adding a new gateway, not changing the default gateway.