Custom firmware is just a set of patches that are applied at runtime when you boot an emunand (or a sysnand, for that matter). You don't need to use separate emunands for separate custom firmwares.
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Whats even the point of duel emunands?
The only reason I can think of having more than one emunand for is if you wanted to have multiple regions on the same console. For example, I've seen some people go with a setup where they have a 9.2 sysnand, an updated emunand, and a second updated emunand of another region.
But imo arm9loaderhax all but killed that particular use case. It's much more practical to have a 10.7 sysnand and a 10.7 region changed emunand instead of going the multiple emunands route.