I just wanted to connect USB floppy to this motherboard.
This MB includes standard external usb ports and 2 internal standard usb headers. It also contains one internal usb connector(not header) J1J2 which is called "internal smart module connector".
What is the difference between this one and all other usb ports - is it good to connect my usb floppy to it ?
That connector is same as other USB connectors. If you can find a way to route the cable and mount the drive, yes you can connect USB floppy to it.