This is done in the Supplier Agreement page, in tab Valid Sites.
When the supplier agreement is used as a group agreement, the sites must be specified on the supplier agreement. If it is a local agreement, the owning site will appear by default on this tab; it cannot be changed.
To have a supplier agreement for just one site, when it is not the owning site, enable the Group Agreement option on the header and simply enter one site on the Valid Sites tab.
The supplier agreement can be used for all the entered sites, if no special conditions are set up on the part or supplier assortment lines.