You have two options: since both of your systems are modded, you can can either rip your installed games with
GodMode9 to make cia files so you can install them on the other 3DS (or skip it if you still have those cias on your sd card or if you choose to redownload them instead..).
And backing up ALL your
saves with
Checkpoint, this is a must since saves are encrypted, you can't use them on the other system straight away.. (Checkpoint has a batch backup option to do it in one click..
)
The 2nd method is doing a
system transfer, it's up to you which one you should choose, but if you want to keep both systems as is then do the 1st method.