You can adjust the AG effect of the craft in the CARD system once you have opened the respective cards up to use.
The AG effect can also be dependent on other craft configurations, like if you were to build a craft loadout that was specifically built for combat, with 'Heavy Hull' card employed, along with a few others, it's a balancing act.
It was frustrating when the CARD system first made a appearance, as it seemed just as you got your head around what seemed to be a pretty good configuration, there would be a update and some cards would be removed and replaced with others, or some CARDS effects would be amplified or lessened.

TBH I just tested till I found a overall CARD setup that could be applied to each craft so I could make it through Campaign, and left it at that, I probably could get a lot better performance out of the crafts if I did more testing and swapped a few things around, but in the back of my mind I knew the day would come when FF V2 [Now PACER] would be released, and a lot of things would have changed and I would have to do it all again anyway, so I just didn't torture myself doing it.
Besides, a lot of the CARDS seem to have little effect on one craft, but when applied to another, that effect is much greater, something you don't really find out unless you do a LOT of testing.

I have asked if there will be some form of craft testing area within the game, where you can quickly swap out different CARDS and see the difference more easily, without having to save the configuration, apply it to a craft then start a race to see the effect, it's the need to go through that laborious process that can put people off.