Assuming you're using a CFW of some sort, and not Gateway: if you're on O3DS the update should work fine if your emuNAND is on 9.6 or higher. On N3DS, the update requires editing the update to set the minimum firmware version to 9.5, since the CFWs currently available don't seem to spoof the firmware version like Gateway does (or at least, Reinand doesn't). Note that a modified update is out in the wild, so you don't have to do the edit for N3DS anymore.
If you're on Gateway, the update should work straight away regardless.