An FQHC is a Federally Qualified Health Center, which means you have to bill based on specific Medicare Guidelines that are set up for FQHCs. I have been coding/billing for an FQHC for a long time.
Everything is based on encounters with the physician/clinician. Certain services are not-billable unless there is a face-to-face encounter with the clinician. Visits/encounters must be billed along with a G-code and Medicare pays on the G-code based on the rate set up for your geographical area (GAF). These are billed to Medicare Part A and paid as part of the FQHC. Many services that are provided along with the visit (urinalysis, A1c, PFT, etc.) are split off of the visit/encounter and billed separately to Medicare part B and paid fee-for-service.
The practice I work for is an FQHC and we are set up to bill as an FQHC with Medicare, Medicaid, and the Marketplace/Exchange plans. We bill commercial payers as a normal or non-FQHC services.
There are some good resources out there. Here is one I use:
https://www.cms.gov/Center/Provider-Type/Federally-Qualified-Health-Centers-FQHC-Center.html
Also, it is good to get in touch with other FQHCs in your area.
Best of luck!