I'm a dad in San Diego, but of a five year old.
Living near the airport is going to be expensive: Point Loma, Ocean Beach, Banker's Hill, Downtown, Clairemont, Mission Beach, Pacific Beach, La Jolla and Del Mar all offer a variety of rental options, but with two middle schoolers I'd imagine you'd want a larger house which gets pricy real fast in these areas.
I live right on the edge of San Diego near La Mesa, in an area called Rolando Park and we love it. Bought our house for 315,000 in 2011, and now has risen to $420,000 in value. Rents in this area (92115) are generally $1800+ for a 3 bedroom, but you'll get a house and the commute to the airport is not bad at all, maybe +/- 20 minutes down the 94.
Driving from the northern county down the 5 will be brutal if it is during the normal commuting hours.
I'm not overly familiar with Mira Mesa, Clairemont Mesa, Kearny Mesa, University City, and Sorrento Valley. These communities are generally east of 5, south of 56, and west of 15. There might be something there that is more affordable.
Can't speak to schools as my kid is just about to start. You can apply to transfer to any school within the SDUSD, but there is no guarantee that a transfer will be granted.
Good luck and let me know if I can explain anything further.