If your goal is to have a clean sysMMC for online play and a dirty emuMMC for hacks, then you should update your sysMMC through the system settings. If you don't want to burn your fuses, and you already have AutoRCM installed, you should be running Atmosphere on your clean sysMMC when you update the system in the system settings. This will make it so AutoRCM is not removed.
If you do not plan on using a clean sysMMC for online play, then you shouldn't bother with an emuMMC.
There isn't much of a reason to worry about your fuse count, to be honest. The only reason to care about your fuse count is so you can downgrade for future exploits, but that doesn't seem likely to happen anytime soon (if ever), and the RCM exploit will last you forever if your Switch is RCM exploitable. Other than that, the fuse count doesn't really matter, since the fuse count checks can be bypassed using fusee-primary or Hekate.