I can speak for the summoner pet. Not sure if the scholar pet works the same or not.

When you summon the egi, immediately hit 'Steady'. This will stop your pet from doing anything but follow you around. At the first mob you attack, hit 'Obey' and your pet will only use his auto attack skill. The other skills you can then manually cast yourself. These skills are not affected by your cool downs, you can cast them whenever they are up.

Once you have hit 'Obey', your pet will stay in that mode until you summon another pet.