After farming a set of Atma I'm working on upgrading my Omnilex for Scholar.

I'm not sure though if when doing the dungeons when do I need to equip my Omnilex Atma for credit. Do I need to have it equipped the entire run? Can I use my Book of Diamonds for the dungeon and switch to the Atma for credit on the last boss? Is there some way to run those without having to take a downgrade on my healing?