Can I change each Print Facility to only see the Customers that they deal with?

Yes, you can do this via admin groups.
 
a. Create an admin group for each print facility in Preferences > Admin Groups. Set the permissions for this admin group to "Not Set" for every permission.
b. Make admin users members of the admin group that corresponds to their print facility in Preferences > Admin Users.
c. For each site that the Print Facility needs to manage, go to the site groups for that site (Sites > [Site name] > Site Groups). Click on the "Admin Groups" link at the top of the page. Click the pencil icon to edit the print facility's admin group. Set the permissions to "Allowed."
d. For each site that the print facility does not manage, go to the site groups for that site. Click on the "Admin Groups link at the top of the page. Click the pencil icon to edit the print facility's admin group. Set the permissions to "Not Set."
 
 
Related Article: Ch. 021. Admin Groups