1. Not sure if it's the same for running older versions, but with rxtools 3.0, when you're booting into it hold L to get into the boot menu and from there you can backup your NANDs, or you can backup sysNAND from the Gateway launcher.
2. As long as you're using an O3DS (N3DS support is coming) you can update to 10.3 emunand by making sure you're in emunand (on rxtools 3.0 it should say RX E before the version number) and updating from there OR download the update files from that iso site or using 3DNUS and (making sure you're in emunand) install using either BigBlueMenu or sysupdater.