Salvatore,
We assume you have a Yamaha FC7 as your Foot Controller pedal, plug it into the FOOT CONTROLLER jack on the back panel.
We assume you have a Yamaha FC3A or FC4A as your Sustain pedal, plug it into the SUSTAIN pedal jack on the back panel.

By default, the FC7 will act as an Expression pedal to control Output level
By default, the FC3A/FC4A will act as your Sustain pedal. Automatically.

If you would rather use the FC7 as a programmable pedal, where you decide on a per Program basis what it will control... then you should set the Foot Controller 1 to send cc004. This will make it equal to FOOT CONTROLLER 2.

This device, Foot Controller 2 can be programmed on a per VOICE basis what it controls, it can control wah-wah on one Voice, be Rotary Speaker Speed on another, and volume on another, you choose what cc004 is going to control.

Unfortunately, you don't mention what you need it to control and you don't mention on what Voice you want to use it.