If it doesn't work for whatever reason then you can put it back and it's fine.
It *may* be a separate controller and it may be the case that that controller is disabled currently. If this happens then you need to put it back on the 3Gbps port, boot in, install the driver for that other controller and then move it to the 6Gbps port. If they're all on the same controller then just move it, it's fine.