You can do both. You can make an EBOOT for each disc, which will reduce file size, or you can put all the images into one EBOOT, which, while bigger, will mean you'll never have to swap files. I personally prefer the former, but it's really up to you.
That's the weird part. My switch is a lite one, mod-chip, SXOS 10.2.0. I followed a recent video showing how to migrate using the same model as I do, everything was fine until I hit the launch button and then atmosphere and this error appeared