Need help with T4i settings when using 600EX-RT flash

I just received my Yong Nuo 600EX-RT flash for my Canon T4i w/18-135 STM and used it for the first time at a family event today. For the last several years, I have gotten somewhat comfortable in manual mode for still shots where I have time to set up, but mainly use Av mode without any flash for most situations involving people. Being my first experience with an external flash and not really understanding why it does what it does in Av mode, I decided to use Auto (A+) mode to make sure the pictures would come out.  What a mistake!  Let me explain and please help.

What is consistent about the photos is that auto mode chose high ISO's and low apertures in almost all situations, so although my lighting is great (maybe overexposed a bit) my depth of field is terrible and of course more noise than desired.  Many shots are unusable because the plane of focus is so shallow that only one person (or one row of people in a group photo) is in focus.  I see the red focus grid and hear the focus lock beep but why, knowing the flash is going to fire, does the camera still choose settings like it doesn't know the flash will fire?

What mode should I be using on the camera dial for easy external flash shooting like this?  Do I have some flash or camera settings set incorrectly?  I am in ETTL mode on the flash.

Thanks for any help in heading me in the right direction.  Very disappointing photos today.