Yes you will still need to head to international desk for check in. Checking in online just reserve your boarding number and will not issue a boarding pass. They are extremely strict at BWI about the 60 minutes check in for international flights so do not try to cut it close. I have seen people having to reschedule.
There is a A-List preferred line at the international check in area and you will now get precheck. Everything else besides the checking in at the desk is standard Southwest ops.