In the 4U CE-C4 Chassis, can I use all 5.25 inch bays with an extended motherboard inside?
This depends on the external 5.25" devices used.
Because the CE-C4 is a compact and therefore short chassis there is limited space inside.
When you use an extended ATX motherboard ( SSI EEB3.0, 12x13 inch ) you can only use short 5.25 inch devices or they will interfere with higher components on the motherboard.