If I have unlinked the sysnand unlinked with emunand, I just have to install the gba games in cia format in both, emunand and sysnand?
I have them unlinked too.
I boot into devmode through rxtools, I then install my gba cia's through fbi running in sysnand devmode to sd (or nand if it's dsiware).
Afterwards I boot into emunand and once again install the gba cia's to emunand's sd.
That last step is only necessary if you want to boot gba/dsiware in emunand, which is easier for me than having to boot into sysnand with sigchecks disabled every time for gba.
This is of course assuming you patched your agb_firm properly.