Is there a way to make the cpu have good skills equiped ? I have the whole game set to random level and random abilities or do I have to assign them in the patcher myself ? example a knight that has all his or her skills ?
Increase the level of their job, that should give them access to more of their skills. To do this, check out the ENTD of the battle you want to work on and go down the the Jobs Unlocked tab, the number to the right dictates what that job level is, so just increase that.
Another roundabout way is to reduce the JP costs of the skills you want them to use.