Benefits of unlinking the nands are that you'll no longer have to unwrap installed games / apps (cias) each time you boot into emunand & if you go into the Data Management from the emunand, all installed dlc / updates (that were installed via cia) won't be wiped.
You can either drag and drop replacing everything, or you can remove all of the files used by Reiand, then drop the new files in their place.
You'll install games in cia format using a title manager such as Devmenu or BigBlueMenu.
When you reboot, you'll be in Sysnand, there's no coldboot > Emunand for the 3DS
That's up to you, N3DS users can update to 9.5.0-23. If you look on the pastebin, there's a link on how to do this.