The latest R4 3DS Firmware has been released for the official R4 3DS cards from http://www.r43ds.org You can download the new firmware from their website. You should use this firmware if you have not yet updated you 3DS or 3DS XL to the 6.3.0 system software.
Prior to updating your console itself, download and copy the new firmware files over to your micro SD Card. once that is completed, put your r4 3ds in to your Nintendo 3DS and 3DS XL system, and run the R4 at least once, so that it uses the new firmware. Once you've done so, you can feel free to update your 3DS or 3DS XL to the new 6.3.0-12 update without any issues.
