Familiar Settings contains all the settings related to Training, Upgrading, Enhancing and Skills of Familiars.
Pact options:
Open Pacts (includes New Familiars) - Opens merged or obtained familiar packs automatically.
Merge Pacts - Enabled merging of unlocked pacts.
You can select the pact(s) you wish to merge with the check boxes to the left of this option. Note: You must have the research unlocked to be able to train higher level pacts.
Distribute Heroes Evenly - When training familiars in the Gym, distribute the heroes evenly across all familiars being trained.
Daily Fragment Limit - Used to set how many fragments should be spent on upgrading skills daily. the more fragments used for upgrading in a given day, the more expensive it becomes until the daily reset.
Familiars Grid & Familiar Options
The grid at the bottom of the page can be used to select options for a familiar, multiple familiars can be selected at the same time.
Selecting the familiar(s) enabled the Familiar Options panel which can be used to set the settings for each one.
Train - Send this familiar to the gym to be trained.
Train Skills - When a familiar has reached maxed level, continues to send it to the gym to level up a random skill.
Use Exp Items - Allows obtained EXP items to be used on that familiar to level it up.
Shatter Extra Runes - when you have more runes then is required to upgrade a familiar, shatter the extra runes to gain Fragments.
Use Skills - When a familiar's skills becomes available, use its skill.
Upgrade Skills - Use Fragments to upgrade the familiars skills.
Enhance - Allows runes to be used to upgrade the stage of the familiar.
Double Click Menu:

The double click menu allows you to see the Skills available and there status. You can also use "Dont Upgrade" to prevent fragments being used to upgrade that skill.
Double clicking on a skill within this window will manually use the skill (if it is non-passive)