Firstly, don't use sysUpdater while using Gateway sysNAND mode, or you'll brick your 3DS.
If you already have an emuNAND set up with Gateway (classic mode, yes), then just use a .3ds version of DevMenu/BBM/FBI to install a CIA of the CIA installer you prefer.
If you don't have an emuNAND, I'm not really sure how it works with the newest Gateway updates, but on older ones you held B while choosing Gateway mode, which would boot you into sysNAND with signature checks patched (but it's still not safe to use sysUpdater there). From there you can install the CIA manager using the .3ds version of DevMenu/FBI.
You'll want to look into getting minipasta or RxTools dev mode (also called Pasta mode in newer builds) to be able to use sysUpdater safely. Updating your sysNAND in Gateway sysNAND mode causes bricks (just restating this for emphasis).