If you give yourself an hour to get to HKIA, give yourself double to get to Shenzhen airport - especially the first time. I use it a lot, but if travelling with a family, maybe I would pay extra for the convenience of travelling from HKIA.
Besides ctrip, also look on elong and travelzen. qunar is good, if you can read Chinese, and if you are in the Mainland so you can book and pay for the cheaper fares. But, internal airfares seem quite high this year in China. Consider flying to Tianjin and then getting the fast train to Beijing if the fare is very different.