If you will be located in Encanto, your closest private schools would be Mator Dei down south in the East Lake area or St. Augustine in North Park(the closer of the two). Both have wonderful scholastic programs and are aggressive about their sports programs. There are other schools obviously, but these two, I believe, are your closets options. Private middle schools...St. Patricks in North Park is a great school with a record of some 50 years plus. Available if you would like more information. Happy New Year!
There are many private schools from which to choose. You can use the Great Schools link I provided to start your research (you can reach me via my profile if needed). Since your kids are in middle and high school, just uncheck the boxes on the left of the web page for preschool and elementary.
I've read that some parents like the Horizon schools (Christian), Francis Parker and La Jolla Country School. But, there are some really good public schools here too, so don't rule anything out until you do some research, and talk or correspond with other parents.
Let me know if you have any other questions regarding your move here. I know Encanto well, and the many other neighborhoods and cities here in San Diego.