I'm also relatively new to any FSWs. But based on what I've learned with an FGT as a controller connected to the first FSW over fortilink then another FSW over ISL between two FSWs, I can tell you shouldn't try configuring those FSWs directly, which might conflict/confuse the controller FGT.
What I can tell with this arrngement is:
- All VLANs you configure on the FSWs (via the FGT's controller in GUI or CLI (under config switch-controller)) need to come to the FGT's fortilink port, which is automatic.
- "auto-ISL" (configured by default) automatically connects between FSWs and passes all VLANs configured under the switch-controller regardless it's actaully used or not.
- In the FSW world, these are not called as "trunk" while the term "trunk" is used to refer to LAG/LACP ports.
- Hidden VLAN ID 4094 is used inside of each FSW for the management interface, called "internal", and this VLAN is set as the native VLAN on the fortilink as well as the ISL interface port.
Again, once a FSW is authorized at the controler FGT, don't try configuring each FSW directly. Use direct CLI only for troubleshooting purposes.