actually, it should be working on the latest nightly.
Edit: but the easy way is to just use browser hax and then install FBI.CIA from FBI.3dsx.
If it won't work like that from emunand, then you'll need to do it on sysnand, then format emunand again. You can always backup sysnand first then flash back the original after you've made the emunand...
And to save the step of copying everything off of your card then copying it back, you can simply install it to sysnand, then make a backup, then use emunand tool to inject that nand directly into emunand. (but you may want to unlink nands after that anyway...)