How do you raise a pets aptitude?
1) Merge a pet that has a higher Aptitude than your Main (agent) pet into it. Blue Rune Pet Eggs work well for this as they tend to be low level and high aptitude.
2) Merge other pets into your main (agent) pet to build training points, the buy or farm golden eggs and buy the potion from the pet trainer inside the ranch. Each potion costs 3 golden eggs, and each raises the pet's aptitude by 1 point.
I did a combination of both to raise my pet's aptitude to 100. Some people are trying to figure out the cheapest way to get a pet's aptitude to 100 by the lowest level possible. This is because each time your pet gains a level, the higher it's aptitude the higher the stat value gain for each level.
I personally didn't worry about that too much. I got my pet's aptitude to the low 90's by lvl 15 then fed it golden egg potions to get it to 100. My pet is currently lvl 18 with 100 Apt. Good enough for me.