As they are two seperate nands, no, what you do on one nand is independent from the other. To do something like that you'd have to find a way to force the switch to mount two nands at the same time, which I don't think is possible at all.
I guess you could backup the sysnand from rcm, then create a second emunand partition from that sysnand backup, then use cfw on the new emunand to backup the games.
There's also a windows tool that can extract games/updates as nsp files when you mount your nand/backup to the pc (I never could get it to work myself, but plenty others have managed).
Can't remember what it's called, but just look in the tools or tutorials section and you should find it.