I can't see a way of splitting Ally Favour for the purposes of fortifying. This means if we have more flavour than a given Ally requires for max level, the only option at present appears to be to burn the excess since the system doesn't allow us to tell it how much we actually want to use. It's all or nothing. Disregard. I didn't know that holding shift while hovering over it brought up the split option in the fortify menu.
I'm at rank 4, only need 1170 Ally Favor I have 4930 Ally Favor, I can add single favor at time, but it's 1170 times. If I click the whole thing it eats WHOLE 4930 Ally Favors. At least with the Artifact upgrades. Maybe you need to look into it and get a better Upgrade system.
You can add it in pretty fast holding the d pad down and the L3 toggle down if on ps. It's still annoying but goes much quicker. Too quick if you hold too long lol. Typing in an amount would be much better