If you're working in Makati CBD, and living in a condo is not an option, definitely I'd pick the South. I grew up in the south and enjoyed the suburb feel, and back then toll wasn't exorbitant yet. But even now, living in the south isn't so bad if you can deal with the toll. The advantage is that houses in BF Homes are still much cheaper than houses in QC (Maginhawa area), so this should offset your toll costs.

Traffic is pretty bad though during rush hours along Sucat Road (or Zapote if you decide in Las Pinas), but not as bad as QC traffic. Also, during weekends, there's no need to leave the south as everything is in Alabang.

Biggest drawback is if you have some business to attend to in QC, you'll bear EDSA/C5 traffic, but if it's just BGC or Makati, it's not so bad. Another thing to consider is that IMO schools are still better in the North. I studied in Zobel when I was younger and I can honestly say that AGS/AHS is better (less conyo kids, better education). You also get to be near Pisay (if you consider that option for your kids).