Facility billing will be on a UB04. Use H codes. The facility will be the billing facility and rendering provider. You can put the clinical director/medical supervisor in the supervising physician section, but you don't have to.
If you are billing physician or professional fees separate, use 9 codes or h codes but put them on a HCFA. For example, if your billing a doctors medical assessment separate of the facility, use an EM code on a HCFA. Any LISAC billing goes on a HCFA.