Re separate applications, no - all applications for a place at secondary school have to be made via your CAF.
With regard to just naming WHSB and SHSB, some will do that, in your position (and ours, fortunately
) it may be tempting. However, since we do not have rankings and don't know how many in-catchment boys qualified, personally I will still be filling in all the places on our CAF. At the moment, DS2's list goes SHSB / WHSB / Cecil Jones / Sweyne Park / King John. We will be going back to SHSB and WHSB, though and may have to rethink fifth preference if he has not done well in the King John test.