Before doing this how do I back up my game saves, just in case something goes wrong?
Best way to backup saves is JKSV
Most of my games are xci will I be able to play them or do I start looking for NSPs?
You can install XCIs the same as NSPs. No need to re-download everything.
Would it be easier to format sd card and start fresh with new emunand with atmosphere?
Only marginally easier. Ideal state would be to work with a complete bit-for-bit backup or start from scratch with a blank fresh card. Neither is a requirement though.
Thanks