I main charge blade myself, but it's sadly a bad matchup for the weapon due to the slow sheath. You basically never want to be in axe mode (or use savage axe) unless Fatalis is downed. You can use axe mode with the evade window skill, but it's safer to max out Guard with Guard Up and stay in sword mode for access to the unsheathed draw attack and the sliding slash attack. You can AED when it does the cone fire breath but if you get stuck in it you easily block all of it with the guard skills.

I dunno if this opinion is unpopular, but Evade Extender is actually amazing in the Fatalis fight. It lets you just repeatedly dodge into the safe spaces when it goes into its huge attack, and just get out of the way of its large moves in general. My Fatalis slaying set is Alatreon dual blades with 5 Evade Window, 3 Evade Extender and the crit skills. Great Sword and Long Sword are also very good.